U.S. patent application number 11/639663 was filed with the patent office on 2007-11-29 for droplet-based affinity assays.
Invention is credited to Allen E. Eckhardt, Vamsee K. Pamula, Michael G. Pollack, Vijay Srinivasan.
Application Number | 20070275415 11/639663 |
Document ID | / |
Family ID | 38749982 |
Filed Date | 2007-11-29 |
United States Patent
Application |
20070275415 |
Kind Code |
A1 |
Srinivasan; Vijay ; et
al. |
November 29, 2007 |
Droplet-based affinity assays
Abstract
The present invention relates to droplet-based affinity assays.
According to one embodiment, a method of detecting a target analyte
in a sample is provided, wherein the method includes: (a) executing
droplet operations to combine affinity-based assay reagents on a
droplet microactuator with a sample potentially comprising the
target analyte to generate a signal indicative of the presence,
absence and/or quantity of analyte; and (b) detecting the signal,
wherein the signal corresponds to the presence, absence and/or
quantity of the analyte in the sample.
Inventors: |
Srinivasan; Vijay; (Durham,
NC) ; Pamula; Vamsee K.; (Durham, NC) ;
Eckhardt; Allen E.; (Durham, NC) ; Pollack; Michael
G.; (Durham, NC) |
Correspondence
Address: |
WARD AND SMITH, P.A.
1001 COLLEGE COURT
P.O. BOX 867
NEW BERN
NC
28563-0867
US
|
Family ID: |
38749982 |
Appl. No.: |
11/639663 |
Filed: |
December 15, 2006 |
Related U.S. Patent Documents
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60745058 |
Apr 18, 2006 |
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60745039 |
Apr 18, 2006 |
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60745059 |
Apr 18, 2006 |
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60745914 |
Apr 28, 2006 |
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60745950 |
Apr 28, 2006 |
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60746797 |
May 9, 2006 |
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60746801 |
May 9, 2006 |
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60806412 |
Jun 30, 2006 |
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60807104 |
Jul 12, 2006 |
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60745043 |
Apr 18, 2006 |
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Current U.S.
Class: |
435/7.4 ;
436/2 |
Current CPC
Class: |
B01F 13/0071 20130101;
B01F 13/0076 20130101; B01L 2200/0673 20130101; B01L 2400/0448
20130101; B01L 3/0268 20130101; B01L 2300/0864 20130101; B01L
2400/043 20130101; G01N 15/1484 20130101; B01L 2300/0867 20130101;
B01L 2400/0436 20130101; B01L 2400/0406 20130101; B01L 2400/0421
20130101; B01L 2200/027 20130101; G01N 2015/1006 20130101; B01L
2300/0654 20130101; B01L 2300/1827 20130101; B01L 2200/0668
20130101; B01L 2400/0442 20130101; B01L 2300/089 20130101; B01L
3/502784 20130101; B01L 2200/148 20130101; B01L 2300/0816 20130101;
G01N 33/54373 20130101; B01L 3/502761 20130101; B01L 7/525
20130101 |
Class at
Publication: |
435/007.4 ;
436/002 |
International
Class: |
G01N 33/573 20060101
G01N033/573; G01N 33/48 20060101 G01N033/48 |
Goverment Interests
1 GRANT INFORMATION
[0002] The work leading to this invention was supported at least in
part by XXX Grant Nos. YYY. The United States Government may have
certain rights in the invention described herein.
Claims
1. A method of detecting a target analyte in a sample, the method
comprising: (a) executing droplet operations to combine
affinity-based assay reagents on a droplet microactuator with a
sample potentially comprising the target analyte to generate a
signal indicative of the presence, absence and/or quantity of
analyte; and (b) detecting the signal, wherein the signal
corresponds to the presence, absence and/or quantity of the analyte
in the sample.
2. The method of claim 1 wherein one or more of the droplet
operations is effected on a droplet microactuator.
3. The method of claim 1 comprising an electric field-mediated
droplet operation.
4. The method of claim 1 comprising an electrode-mediated droplet
operation.
5. The method of claim 1 comprising an electrowetting-mediated
droplet operation.
6. The method of claim 1 comprising an dielectrophoresis-mediated
droplet operation.
7. The method of claim 1 wherein the affinity-based assay reagents
comprise immunoassay reagents.
8. The method of claim 1 wherein the detecting step comprises
detecting a signal from a droplet on a droplet microactuator.
9. The method of claim 1 wherein the detecting step comprises
detecting a signal from a surface on a droplet microactuator.
10. The method of claim 9 wherein the surface comprises a surface
of a bead.
11. The method of claim 10 wherein the bead is magnetically
responsive.
12. The method of claim 10 wherein the bead is not substantially
magnetically responsive.
13. The method of claim 9 wherein the surface comprises a surface
of the droplet microactuator.
14. The method of claim 9 wherein: (a) the surface comprises
scintillant molecules and capture molecules; and (b) the droplet
operations comprise contacting a sample droplet comprising a
radiolabeled molecule having affinity for a capture molecule with
the surface, such that when a radiolabeled molecule is bound to a
capture molecule, radioactive particles interact with the
scintillant molecules to produce light.
15. The method of claim 14 wherein the surface comprises a surface
of a bead or a surface of the droplet microactuator.
16. The method of claim 9 wherein: (a) the surface comprises a
roughened metal film comprising a capture antibody on a surface
thereof; and (b) the droplet microactuator comprises electrodes
configured for transporting a droplet into contact with the
roughened metal film.
17. The method of claim 16 wherein the roughened metal film
comprises a silver or gold film.
18. The method of claim 9 wherein the surface is labeled with Raman
reporter molecules.
19. The method of claim 9 wherein the signal comprises Raman
spectra.
20. The method of claim 7 wherein the signal measured corresponds
to unoccupied binding sites on an antibody.
21. The method of claim 7 wherein the signal measured corresponds
to occupied binding sites on an antibody.
22. The method of claim 7 wherein the affinity-based assay reagents
comprise an antibody immobilized on a surface.
23. The method of claim 22 wherein the surface comprises a solid
phase within a droplet on the droplet microactuator.
24. The method of claim 22 wherein the surface comprises a surface
of the droplet microactuator.
25. The method of claim 22 wherein the surface comprises a bead
disposed in a droplet on the droplet microactuator.
26. The method of claim 25 wherein the bead is a magnetically
responsive bead.
27. The method of claim 25 wherein the bead is not substantially
magnetically responsive.
28. The method of claim 25 wherein the affinity-based assay
reagents comprise a labeled analyte tracer.
29. The method of claim 28 wherein the labeled tracer generates a
signal only when bound to the affinity reagent.
30. The method of claim 28 wherein the labeled tracer generates a
signal only when not bound to the affinity reagent.
31. The method of claim 25 wherein the droplet operations effect a
competitive affinity-based assay protocol.
32. The method of claim 7 wherein the affinity-based assay reagents
comprise an antibody which is selective for the target temperature
zone analyte.
33. The method of claim 7 wherein the affinity-based assay reagents
comprise two or more antibodies, each selective for a specific
epitope or region of the target analyte.
34. The method of claim 7 wherein the affinity-based assay reagents
comprise two or more antibodies, including a first antibody
selective for the target analyte and a second antibody selective
for the first antibody.
35. The method of claim 25 wherein the affinity-based assay
reagents include a labeled antibody.
36. The method of claim 35 wherein the labeled antibody comprises a
radioactive isotope.
37. The method of claim 25 wherein the affinity-based assay
reagents include an antibody conjugated to an enzyme capable of
catalyzing a detectable reaction.
38. The method of claim 36 wherein the detectable reaction result
in a colorimetric, fluorescent and/or luminescent property or
signal.
39. The method of claim 35 wherein the droplet operations comprise
a droplet-based washing protocol for separating labeled antibody
which is bound to the analyte from labeled antibody which is not
bound to the analyte.
40. The method of claim 39 wherein the labeled antibody which is
bound to the analyte is also bound to a surface and the
droplet-based washing protocol comprises: (a) removing droplets
from the surface which comprise labeled antibody which is not bound
to the analyte; and (b) adding droplets to the surface which do not
include labeled antibody which is not bound to the analyte.
41. The method of claim 40 wherein the surface comprises a surface
of a solid phase in contact with a droplet on a droplet
microactuator.
42. The method of claim 40 wherein the surface comprises a surface
of a droplet microactuator.
43. The method of claim 7 wherein the affinity-based assay reagents
comprise reagents for conducting an assay type selected from the
group consisting of sandwich assays, immunometric assays,
immunometric assays, capture bridge assays, direct class capture
assays, indirect class capture assays, assays for small molecules,
noncompetitive assays for small molecules, ambient analyte assays
and free analyte assays.
44. The method of claim 43 comprising conducting two or more of the
assay types simultaneously on a droplet microactuator.
45. The method of claim 43 comprising conducting three or more of
the assay types simultaneously on a droplet microactuator.
46. The method of claim 7 further comprising conducting droplet
operations to develop a calibration curve.
47. The method of claim 7 wherein: (a) the droplet operations bring
a capture antibody and a labeled detecting antibody into contact
with the sample to yield a capture antibody-analyte-detecting
antibody complex in the presence of the analyte; (b) droplet-based
washing protocols are employed to separate the capture
antibody-analyte-detecting antibody complex from unreacted
components of the sample and/or unreacted excess antibody; and (c)
the detecting step comprises detecting a signal from the capture
antibody-analyte-detecting antibody complex.
48. The method of claim 7 wherein the droplet operations employ a
sample from a source selected from the group consisting of whole
blood, lymphatic fluids, serum, plasma, sweat, tear, saliva,
sputum, cerebrospinal fluids, amniotic fluids, seminal fluids,
vaginal excretions, serous fluids, synovial fluids, pericardial
fluids, peritoneal fluids, pleural fluids, transudates, exudates,
cystic fluids, bile, urine, gastric fluids, intestinal fluids,
fecal samples, fluidized tissues, fluidized organisms, biological
swabs and biological washes.
49. The method of claim 7 wherein the affinity-based assay reagents
comprise an antibody.
50. The method of claim 49 wherein the antibody is immobilized on a
surface.
51. The method of claim 50 wherein the surface comprises a surface
of a bead.
52. The method of claim 51 wherein the bead is magnetically
responsive.
53. The method of claim 51 wherein the bead is not substantially
magnetically responsive.
54. The method of claim 50 wherein the surface comprises a surface
of the droplet microactuator.
55. The method of claim 50 wherein the droplet operations comprise
immobilizing an antibody on the surface to provide an immobilized
antibody.
56. The method of claim 55 wherein the droplet operations comprise
contacting an antibody in a droplet with a surface of the droplet
microactuator sufficient to result in immobilization of the
antibody on the surface.
57. The method of claim 55 wherein the droplet operations comprise
contacting an antibody in a droplet with a surface of a bead
sufficient to result in immobilization of the antibody on the
surface.
58. The method of claim 57 wherein the contact is achieved by
droplet operations comprising combining the droplet comprising the
antibody with a droplet comprising a bead.
59. The method of claim 55 wherein the droplet operations further
comprise washing the surface to remove excess antibody.
60. The method of claim 55 wherein the droplet operations further
comprise providing the sample as a sample droplet.
61. The method of claim 60 wherein the droplet operations further
comprise exposing immobilized antibody on a surface to a sample
droplet potentially including the target analyte.
62. The method of claim 61 wherein the droplet operations further
comprise washing the surface thereby removing or reducing the
quantity of unbound sample material.
63. The method of claim 50 wherein the droplet operations further
comprise exposing the immobilized antibody to a droplet including a
reporter antibody.
64. The method of claim 50 wherein the droplet operations further
comprise washing away excess reporter antibody.
65. The method of claim 50 wherein the droplet operations further
comprise performing additional steps to produce a measurable
parameter or signal.
66. The method of claim 65 wherein the measurable parameter or
signal comprises an electrochemical property of a droplet on a
droplet microactuator.
67. The method of claim 66 wherein the electrical property
comprises an amperometric, potentiometric and/or conductometric
property of a droplet on the droplet microactuator.
68. The method of claim 65 wherein the measurable parameter or
signal comprises an optical property of a droplet on a droplet
microactuator.
69. The method of claim 68 wherein the optical property comprises
absorbance, chemiluminescence and/or fluorescence.
70. The method of claim 68 wherein the optical property comprises
Raman spectra.
71. The method of claim 65 wherein the measurable parameter or
signal comprises a physical parameter of a droplet on a droplet
microactuator.
72. The method of claim 71 wherein the physical parameter comprises
temperature.
73. The method of claim 71 wherein the physical parameter comprises
emission of radioactive particles.
74. The method of claim 49 wherein the droplet operations further
comprise: (a) exposing the immobilized antibody to a sample droplet
potentially including the target analyte with binding affinity for
the immobilized antibody; (b) washing the immobilized
antibody-target analyte complex thereby removing unbound components
of the sample droplet; (c) exposing the immobilized antibody to a
droplet including a reporter antibody; (d) washing away excess
reporter antibody; and (e) performing additional steps to produce a
measurable parameter or signal.
75. The method of claim 74 further comprising providing an
electronically produced output indicative of the signal.
76. The method of claim 49 wherein the droplet operations further
comprise providing a sample droplet potentially including target
analyte and including a reporter analyte.
77. The method of claim 76 wherein the droplet operations further
comprise exposing the immobilized antibody to the sample droplet so
that the reporter analyte competes with any target analyte for
binding sites.
78. The method of claim 77 wherein the droplet operations further
comprise washing the substrate to remove unbound analyte and
reporter analyte.
79. The method of claim 78 further comprising performing additional
droplet operations to yield a measurable parameter or signal.
80. The method of claim 78 further comprising quantifying bound
reporter analyte, wherein the quantity of reporter analyte is
inversely proportional to the quantity of target analyte.
Description
2 RELATED APPLICATIONS
[0001] This application also is related to and incorporates by
reference related provisional U.S. Patent Application Nos.
60/744,780, entitled "Apparatus and Methods for Droplet-Based
Protein Crystallization," filed on Apr. 13, 2006; 60/745,058,
entitled "Filler Fluids for Droplet-Based Microfluidics" filed on
Apr. 18, 2006; 60/745,049, entitled "Apparatus and Methods for
Droplet-Based Protein Crystallization," filed on Apr. 18, 2006;
60/745,039, entitled "Apparatus and Methods for Droplet-Based Blood
Chemistry," filed on Apr. 18, 2006; 60/745,073, entitled "Apparatus
and Methods for Droplet-Based PCR," filed on Apr. 18, 2006;
60/745,059, entitled "Apparatus and Methods for Droplet-Based
Immunoassay," filed on Apr. 18, 2006; 60/745,914, entitled
"Apparatus and method for Manipulating Droplets with a
Predetermined Number of Cells" filed on Apr. 28, 2006; 60/745,950,
entitled "Apparatus and Methods of Sample Preparation for a Droplet
Microactuator," filed on Apr. 28, 2006; 60/746,797 entitled
"Portable Analyzer Using Droplet-Based Microfluidics," filed on May
9, 2006; 60/746,801, entitled "Apparatus and Methods for
Droplet-Based Immuno-PCR," filed on May 9, 2006; 60/745,054,
entitled "Droplet-Based Multi-Well Plate, filed on Apr. 18, 2006;
60/806,400, entitled "Droplet Microactuator Stamping Platform,"
filed on Jun. 30, 2006; 60/806,412, entitled "Systems and Methods
for Droplet Microactuator Operations," filed on Jun. 30, 2006;
60/807,104, entitled "Method and Apparatus for Droplet-Based
Nucleic Acid Amplification," filed on Jul. 12, 2006.
3 FIELD OF THE INVENTION
[0003] The invention relates to a droplet microactuator and to
systems, apparatuses and methods employing the droplet
microactuator for executing various protocols using discrete
droplets.
[0004] More particularly, the invention relates to droplet-based
affinity assays.
4 BACKGROUND OF THE INVENTION
[0005] The capability to rapidly conduct biochemical and other
assays is critical in a wide variety of fields. For example, rapid
and accurate diagnosis of infectious disease is crucial both for
the effective management of disease in individual subjects and for
ameliorating the public health problems of multi-drug resistant
pathogens and community acquired infections.
[0006] Current PCR-based DNA amplification methods suffer from a
number of drawbacks including high reagent costs, labor intensity
and susceptibility to cross-contamination. Furthermore, compared to
culture, PCR tests are less capable of simultaneously assaying
multiple species, virulence factors, and drug resistant markers.
They often lack sensitivity and cost-effective quantification of
the pathogen. There is a need in the art for improved devices for
nucleic acid detection that would overcome these limitations while
also miniaturizing and automating the technique so that these
assays could potentially be applied at the point-of-sample
collection with minimal training.
[0007] Nucleic acid sequencing is becoming increasingly common in a
variety of fields, such as whole genome sequencing, diagnostics,
pharmacogenomics, and forensics. However, the sequencing field has
been hampered by the expensive nature of sequencing machines. The
development of inexpensive, high-throughput testing systems is
critically important to the spread of genetic testing and the many
advantages that are associated with it. There is thus a need for
new technological platforms that allow one to quickly and reliably
sequence nucleic acids at a reasonable cost. The invention
described herein provides an inexpensive, droplet-based sequencing
system.
[0008] Immunoassays are widely used for clinical diagnostics and
constitute more than a $3 billion market in the US alone.
Immunoassays are among the most sensitive and specific methods that
are routinely used in a clinical laboratory. Immunoassays make use
of the high-affinity and specificity in binding between an antigen
and its homologous antibody to detect and quantify the antigen in a
sample matrix. Heterogeneous immunoassays such as ELISA
(Enzyme-Linked Immunosorbent Assay) are among the most sensitive
and specific clinical analysis methods, and have been widely used
for identification of a large class of antigens and antibodies. For
example, immunoassays are performed, among other things, for
identification of cardiac markers, tumor markers, drugs, hormones,
and infectious diseases.
[0009] Small sample consumption, faster analysis, and complete
automation are three highly desirable features that require
continual improvement in any clinical analyzer. Although
state-of-the-art laboratory immunoassay analyzers offer good
automation and throughput, they require a significant amount of
sample per test (including dead volumes) and lengthy analysis
times. The long assay times and the large size of these analyzers
make them impractical for use in a point-of-sample collection
setting.
[0010] Also, there is considerable variability in the immunoassay
performance, in large part attributed to the techniques being
operator dependent, resulting in difficulty comparing results from
study to study and even within the same study if more than one
laboratory is used. A fully automated and integrated analyzer that
eliminates the operator dependence and standardizes results for the
immune monitoring assays would considerably improve the
interpretation of results from assays.
[0011] Though significant advances have been made in the automation
of immunoassays, these analyzers are prohibitively expensive and
are not affordable in a low-throughput research setting. Lower end
systems with automated plate washers, incubators and integrated
optics still require a skilled technician to perform several key
steps in an immunoassay such as preparing microtiter plates with
antibodies and loading samples onto the plates. This results in
human error due to repeated manual intervention and is a major
source of inter-assay and intra-assay variation.
[0012] There is also a need for point of sample collection testing
in a variety of fields, such as medicine, environmental, and
bioterrorism-related detection fields. As an example,
point-of-sample collection (POC) testing for bedside blood analysis
has improved but remains a key challenge for modern medical care.
Ideally, POC testing would enable the clinicians to diagnose and
implement life-saving technologies in real-time by avoiding the
need for large laboratory facilities. There remains a need in the
art for a lab-on-a-chip that enables simultaneous monitoring of
blood gases, metabolites, electrolytes, enzymes, DNA, proteins, and
cells, on low sample volumes at the POC.
[0013] Microfluidic control of the fluids is an essential
requirement for a successful lab-on-a-chip. Microfluidic systems
can be broadly grouped into continuous-flow and discrete-flow based
architectures. As the name suggests, continuous-flow systems rely
on continuous flow of liquids in channels whereas discrete-flow
systems utilize droplets of liquid either within channels or in a
channel-less architecture. A common limitation of continuous flow
systems is that liquid transport is physically confined to
permanently fixed channels. The transport mechanisms used are
usually pressure-driven by external pumps or
electrokinetically-driven by high-voltages. These approaches
involve complex channeling and require large supporting systems in
the form of external valves or power supplies. These restrictions
make it difficult to achieve a high degree of functional
integration and control in conventional continuous-flow systems,
particularly in realizing a handheld device at the point-of-sample
collection. There remains a need in the art for a point of sample
collection testing system that makes use of droplet manipulations
and especially a system that can accomplish multiple tests or
multiple types of tests on a single chip.
5 BRIEF DESCRIPTION OF THE INVENTION
[0014] The present invention relates to droplet-based affinity
assays. According to one embodiment, a method of detecting a target
analyte in a sample is provided, wherein the method comprises: (a)
executing droplet operations to combine affinity-based assay
reagents on a droplet microactuator with a sample potentially
comprising the target analyte to generate a signal indicative of
the presence, absence and/or quantity of analyte; and (b) detecting
the signal, wherein the signal corresponds to the presence, absence
and/or quantity of the analyte in the sample.
6 DEFINITIONS
[0015] As used herein, the following terms have the meanings
indicated.
[0016] "Activate" with reference to one or more electrodes means
effecting a change in the electrical state of the one or more
electrodes which results in a droplet operation.
[0017] "Affinity" means the specific or non-specific intramolecular
attraction of one molecule for another molecule or for a substrate,
such as the attraction of an antibody for its corresponding antigen
or hapten.
[0018] "Analyte," means a target substance for detection which may
be present in a sample. Illustrative examples include antigenic
substances, haptens, antibodies, proteins, peptides, amino acids,
nucleotides, nucleic acids, drugs, ions, salts, small molecules,
cells.
[0019] "Antibody" means a polypeptide that has affinity for an
antibody can be a polyclonal antibody, a monoclonal antibody, an
anti body fragment, and/or an engineered molecule capable of
binding the corresponding member of a specific binding pair.
Antibodies may be labeled or otherwise conjugated to molecules that
facilitate direct or indirect detection of and/or quantification of
the antibody.
[0020] "Bead," with respect to beads on a droplet microactuator,
means any bead or particle capable of interacting with a droplet on
or in proximity with a droplet microactuator. Beads may be any of a
wide variety of shapes, such as spherical, generally spherical, egg
shaped, disc shaped, cubical and other three dimensional shapes.
The bead may, for example, be capable of being transported in a
droplet on a droplet microactuator; configured with respect to a
droplet microactuator in a manner which permits a droplet on the
droplet microactuator to be brought into contact with the bead, on
the droplet microactuator and/or off the droplet microactuator.
Beads may be manufactured using a wide variety of materials,
including for example, resins, and polymers. The beads may be any
suitable size, including for example, microbeads, microparticles,
nanobeads and nanoparticles. In some cases, beads are magnetically
responsive; in other cases beads are not significantly magnetically
responsive. For magnetically responsive beads, the magnetically
responsive material may constitute substantially all of a bead or
only one component of a bead. The remainder of the bead may
include, among other things, polymeric material, coatings, and
moieties which permit attachment of an assay reagent. Examples of
suitable magnetically responsive beads are described in U.S. Patent
Publication No. 2005-0260686, "Multiplex flow assays preferably
with magnetic particles as solid phase," published on Nov. 24,
2005, the entire disclosure of which is incorporated herein by
reference for its teaching concerning magnetically responsive
materials and beads.
[0021] "dNTP" means deoxynucleotidetriphosphate, where the
nucleotide is any nucleotide, such as A, T, C, G or U. "ddNTP"
means dideoxynucleotidetriphosphate, where the nucleotide is any
nucleotide, such as A, T, C, G or U. It will be appreciated that
unless otherwise specifically indicated, ddNTP can be substituted
for dNTP, and vice versa.
[0022] "Droplet" means a volume of liquid on a droplet
microactuator which is at least partially bounded by filler fluid.
For example, a droplet may be completely surrounded by filler fluid
or may be bounded by filler fluid and one or more surfaces of the
droplet microactuator. Droplets may take a wide variety of shapes;
nonlimiting examples include generally disc shaped, slug shaped,
truncated sphere, ellipsoid, spherical, partially compressed
sphere, hemispherical, ovoid, cylindrical, and various shapes
formed during droplet operations, such as merging or splitting or
formed as a result of contact of such shapes with one or more
surfaces of a droplet microactuator.
[0023] "Droplet operation" means any manipulation of a droplet on a
droplet microactuator. A droplet operation may, for example,
include: loading a droplet into the droplet microactuator;
dispensing one or more droplets from a source droplet; splitting,
separating or dividing a droplet into two or more droplets;
transporting a droplet from one location to another in any
direction; merging or combining two or more droplets into a single
droplet; diluting a droplet; mixing a droplet; agitating a droplet;
deforming a droplet; retaining a droplet in position; incubating a
droplet; heating a droplet; vaporizing a droplet; cooling a
droplet; disposing of a droplet; transporting a droplet out of a
droplet microactuator; other droplet operations described herein;
and/or any combination of the foregoing. The terms "merge,"
"merging," "combine," "combining" and the like are used to describe
the creation of one droplet from two or more droplets. It should be
understood that when such a term is used in reference to two or
more droplets, any combination of droplet operations sufficient to
result in the combination of the two or more droplets into one
droplet may be used. For example, "merging droplet A with droplet
B," can be achieved by transporting droplet A into contact with a
stationary droplet B, transporting droplet B into contact with a
stationary droplet A, or transporting droplets A and B into contact
with each other. The terms "splitting," "separating" and "dividing"
are not intended to imply any particular outcome with respect to
size of the resulting droplets (i.e., the size of the resulting
droplets can be the same or different) or number of resulting
droplets (the number of resulting droplets may be 2, 3, 4, 5 or
more). The term "mixing" refers to droplet operations which result
in more homogenous distribution of one or more components within a
droplet. Examples of "loading" droplet operations include
ricrodialysis loading, pressure assisted loading, robotic loading,
passive loading, and pipette loading.
[0024] "Electronically coupled" is used herein to indicate an
electrical or data relationship between two or more components or
elements. As such, the fact that a first component is said to be
electronically coupled to a second component is not intended to
exclude the possibility that additional components may be present
between, and/or operatively associated or engaged with, the first
and second components. Further, electrically coupled components may
in some embodiments include wireless intervening components.
[0025] "Highlight" used with reference to a user interface or the
like, such as a droplet microactuator map as described herein,
means that a component of the user interface or map may be visually
differentiated, e.g., by a change in color, brightness, shading,
shape, or by appearance/disappearance of a symbol, icon, or other
visual identifier. For example, mousing over or selecting a
representation of an electrode on the user interface or may cause
the electrode representation to change color. Sounds may also
accompany highlighted items to further facilitate user interaction
with the system.
[0026] "Input device" is used broadly to include all possible types
of devices and ways to input information into a computer system or
onto a network. Examples include stylus-based devices, pen-based
devices, keyboard devices, keypad devices, touchpad devices, touch
screen devices, joystick devices, trackball devices, mouse devices,
bar-code reader devices, magnetic strip reader devices, infrared
devices, speech recognition technologies.
[0027] "Magnetically responsive" means responsive to a magnetic
field. Examples of magnetically responsive materials include
paramagnetic materials, ferromagnetic materials, ferrimagnetic
materials, and metamagnetic materials. Examples of suitable
paramagnetic materials include iron, nickel, and cobalt, as well as
metal oxides such as Fe.sub.3O.sub.4, BaFe.sub.12O.sub.19, CoO,
NiO, Mn.sub.2O.sub.3, Cr.sub.2O.sub.3, and CoMnP.
[0028] "Output device" is used broadly to include all possible
types of devices and ways to output information or data from a
computer system to a user or to another system. Examples include
visual displays, LEDs, printers, speakers, modems and wireless
transceivers.
[0029] "Protocol" means a series of steps that includes, but is not
limited to, droplet operations on one or more droplet
microactuators.
[0030] "Select" with reference to a user interactive element, such
as icon, field, or virtual button, displayed on a user interface
means to provide input which results in the execution of
instructions associated with the object. Thus, for example,
selection of a representation of an electrode displayed on a
droplet microactuator map by pointing and clicking on the electrode
representation may result in execution of instructions necessary
for activating the actual electrode and/or instructions necessary
for adding a line of code to a set of instructions which instructs
activation of the actual electrode. Selection may be achieved using
any of a variety of input devices or combination of input devices,
such as mouse, joystick, and/or keyboard.
[0031] "Surface" with reference to immobilization of a molecule,
such as an antibody or in analyte, on the surface, means any
surface on which the molecule can be immobilized while retaining
the capability to interact with droplets on a droplet
microactuator. For example, the surface may be a surface on the
droplet microactuator, such as a surface on the top plate or bottom
plate of the droplet microactuator; a surface extending from the
top plate or bottom plate of the droplet microactuator; a surface
on a physical object positioned on the droplet microactuator in a
manner which permits it to interact with droplets on the droplet
microactuator; and/or a bead positioned on the droplet
microactuator, e.g., in a droplet and/or in a droplet microactuator
but exterior to the droplet.
[0032] "Washing" with respect to washing a surface means reducing
the amount of one or more substances in contact with the surface or
exposed to the surface from a droplet in contact with the surface.
The reduction in the amount of the substance may be partial,
substantially complete, or even complete. The substance may be any
of a wide variety of substances; examples include target substances
for further analysis, and unwanted substances, such as components
of a sample, contaminants, and/or excess reagent. The surface may,
for example, be a surface of a droplet microactuator or a surface
of a bead on a droplet microactuator. In some embodiments, a
washing operation begins with a starting droplet in contact with a
surface, where the droplet includes an initial total amount of a
substance. The washing operation may proceed using a variety of
droplet operations. The washing operation may yield a droplet in
contact with the surface, where the droplet has a total amount of
the substance which is less than the initial amount of the
substance. In another embodiment, the droplet operation may yield
the surface in the absence of a droplet, where the total amount of
the substance in contact with the surface or otherwise exposed to
the surface is less than the initial amount of the substance in
contact with the surface or exposed to the surface in the starting
droplet. Other embodiments are described elsewhere herein, and
still others will be immediately apparent in view of the present
disclosure.
[0033] When a given component such as a layer, region or substrate
is referred to herein as being disposed or formed "on" another
component, that given component can be directly on the other
component or, alternatively, intervening components (for example,
one or more coatings, layers, interlayers, electrodes or contacts)
can also be present. It will be further understood that the terms
"disposed on" and "formed on" are used interchangeably to describe
how a given component is positioned or situated in relation to
another component. Hence, the terms "disposed on" and "formed on"
are not intended to introduce any limitations relating to
particular methods of material transport, deposition, or
fabrication.
[0034] When a liquid in any form (e.g., a droplet or a continuous
body, whether moving or stationary) is described as being "on",
"at", or "over" an electrode, array, matrix or surface, such liquid
could be either in direct contact with the
electrode/array/matrix/surface, or could be in contact with one or
more layers or films that are interposed between the liquid and the
electrode/array/matrix/surface.
[0035] When a droplet is described as being "on" or "loaded on" a
droplet microactuator, it should be understood that the droplet is
arranged on the droplet microactuator in a manner which facilitates
using the droplet microactuator to conduct droplet operations on
the droplet, the droplet is arranged on the droplet microactuator
in a manner which facilitates sensing of a property of or a signal
from the droplet, and/or the droplet has been subjected to a
droplet operation on the droplet microactuator.
7 BRIEF DESCRIPTION OF THE DRAWINGS
[0036] FIG. 1 is a top plan view of a droplet microactuator for use
in amplification protocols in accordance with an embodiment of the
present invention;
[0037] FIGS. 2A and 2B are top plan views of a droplet
microactuator with a single integrated heater and a plurality of
integrated heaters, respectively, in accordance with various
embodiments of the present invention;
[0038] FIG. 3 is a top plan view of a droplet microactuator for use
in nucleic acid sequence analysis in accordance with an embodiment
of the present invention;
[0039] FIGS. 4 and 5 are illustrations showing reaction steps and
droplet operations of an illustrative embodiment in accordance with
the present invention;
[0040] FIG. 6 is a perspective view of a droplet microactuator for
use in conducting immunoassays in accordance with an embodiment of
the present invention;
[0041] FIG. 7 is an illustration showing steps for conducting a
droplet-based sandwich affinity-based assay performed on a droplet
microactuator in accordance with an embodiment of the present
invention;
[0042] FIG. 8 is an illustration showing steps for conducting a
competitive affinity-based assay performed on a droplet
microactuator in accordance with an embodiment of the present
invention;
[0043] FIG. 9 is a perspective view of a biological fluid analyzer
in accordance with an embodiment of the present invention;
[0044] FIG. 10 is a side profile view of a droplet microactuator
loading structure in accordance with an embodiment of the present
invention;
[0045] FIGS. 11-13 are illustrations showing steps for immobilizing
and freeing magnetically responsive beads using a magnetic field in
accordance with various embodiments of the present invention;
[0046] FIG. 14 is an illustration showing steps for immobilizing
and freeing beads using a physical obstacle in accordance with an
embodiment of the present invention;
[0047] FIG. 15 is an illustration showing steps for washing a
droplet microactuator surface in accordance with an embodiment of
the present invention;
[0048] FIG. 16A is a side profile view and FIG. 16B is a top plan
view of a droplet microactuator for transporting droplets in
accordance with an embodiment of the present invention;
[0049] FIG. 17 is a perspective view of a biological fluid analyzer
in accordance with an embodiment of the present invention;
[0050] FIG. 18 is an illustration of droplet microactuator systems
in accordance with an embodiment of the present invention;
[0051] FIGS. 19A and 19B are illustrations of a portable hand-held
analyzer in accordance with an embodiment of the present
invention;
[0052] FIG. 20 is an illustration of a user interface of a droplet
control system in accordance with an embodiment of the present
invention; and
[0053] FIGS. 21A-21D is a side profile view illustrating various
droplet microactuator sensor element configurations in accordance
with various embodiments of the present invention.
8 DETAILED DESCRIPTION OF THE INVENTION
[0054] The invention provides methods, devices and systems for
executing one or more droplet-based biochemical assays. For
example, the invention provides methods, devices and systems for
amplifying nucleic acids, analyzing the sequences of nucleic acids,
conducting affinity-based assays, and/or analyzing components of
bodily fluids.
[0055] In certain embodiments, a protocol of the system may involve
one or more of the following steps in any order which achieves the
detection end of the invention: extracting sample from a subject;
processing the sample for loading onto a droplet microactuator;
loading the sample onto the droplet microactuator; dispensing one
or more sample droplets of the sample for transport on the droplet
microactuator; loading one or more reagents onto the droplet
microactuator; dispensing one or more reagent droplets for
transport on the droplet microactuator; transporting one or more
reagent droplets and/or one or more sample droplets so as to bring
the one or more reagent droplets into contact with the one or more
sample droplets thereby effecting interaction of the reagent with
the sample; detecting an effect of the interaction of the reagent
with the sample; providing output notifying the user of the results
of the detecting step. Examples of biochemical protocols for use
with a droplet microactuator of the invention are discussed in the
ensuing sections.
8.1 Nucleic Acid Amplification
[0056] The invention provides methods, devices and systems for
amplification of nucleic acids in droplets on a droplet
microactuator. A large number of copies of one or more nucleic acid
molecules can be made in a single droplet from a small number of
copies or even a single copy present in the droplet. The methods of
the invention generally involve combining the necessary reactants
to form an amplification-ready droplet and thermal cycling the
droplet at temperatures sufficient to result in amplification of a
target nucleic acid, e.g., by the polymerase chain reaction (PCR).
In some embodiments, a droplet including the amplified target
nucleic acid may then be transported into a subsequent process,
such as a detection process, a process for further manipulation of
the target nucleic acid, and/or a sequencing process (e.g., as
described in Section 8.2). Amplification devices may include a
droplet microactuator and components sufficient to conduct droplet
operations affecting the methods of the invention when the droplet
microactuator is loaded with appropriate reagents. Systems of the
invention may include the droplet microactuator plus system
components designed to facilitate software control of the operation
of the droplet microactuator to execute protocols of the
invention.
[0057] An illustrative droplet microactuator 100 for use in
amplification protocols of the invention is illustrated in FIG. 1.
In this embodiment, multiple fluid ports and/or reservoirs may be
provided, such as sample reservoirs 102, PCR reagent reservoirs
104, and primer set reservoirs 106. Heating areas may also be
provided, such as lower temperature heating area 108 and upper
temperature heating area 110. A sample visualization area 112 may
also be provided, utilizing, for example, a microscope or
photomultiplier tube (PMT).
[0058] In one embodiment, the invention provides a droplet
microactuator and/or system configured and programmed to effect
amplification of a sample in a amplification-ready droplet followed
by capture of the amplified nucleic acid. The amplified nucleic
acid may be treated to denature it into single-stranded nucleic
acid before or after it is contacted with magnetically responsive
beads to permit the single-stranded nucleic acid to bind to the
magnetically responsive beads. Binding, for example, may be
accomplished using a biotin-streptavidin system, e.g., in which the
single-stranded nucleic acid is biotinylated, and the surface
(e.g., beads or droplet microactuator surface) is coated with
streptavidin covalently bound thereto. Amplification reagents may
be washed away using a washing protocol. Various other methods,
devices, systems, and other aspects of the invention will be
apparent from the ensuing discussion.
[0059] It will be appreciated that an important aspect of the
invention involves the ability to conduct droplet operations using
each of the nucleic acid amplification reagents and/or samples on a
droplet microactuator. For example, the invention includes: [0060]
(1) a droplet microactuator comprising thereon a droplet comprising
any one or more of the reagents and/or samples described herein for
conducting nucleic acid amplification; [0061] (2) a device or
system of the invention comprising such droplet microactuator;
[0062] (3) a method of conducting droplet operations on or
otherwise manipulating a droplet making use of such droplet
microactuator or system; and/or [0063] (4) a method of conducting
an droplet-based sequence analysis protocol making use of such
droplet microactuator or system.
[0064] For example, the droplet operations may include one or more
of the following: loading a droplet into the droplet microactuator;
dispensing one or more droplets from a source droplet; splitting,
separating or dividing a droplet into two or more droplets;
transporting a droplet from one location to another in any
direction; merging or combining two or more droplets into a single
droplet; diluting a droplet; mixing a droplet; agitating a droplet;
deforming a droplet; retaining a droplet in position; incubating a
droplet; heating a droplet; vaporizing a droplet; cooling a
droplet; disposing of a droplet; transporting a droplet out of a
droplet microactuator; other droplet operations described herein;
and/or any combination of the foregoing. Various other methods,
devices, systems, and other aspects of the invention will be
apparent from the ensuing discussion.
8.1.1 Samples and Sample Preparation
[0065] The amplification methods of the invention make use of a
sample which includes a nucleic acid template for amplification.
The nucleic acid template may be of any type, e.g., genomic DNA,
RNA, plasmids, bacteriophages, and/or artificial sequences. The
nucleic acid template may be from any source, e.g., whole
organisms, organs, tissues, cells, organelles (e.g., chloroplasts,
mitochondria), synthetic nucleic acid sources, etc. Further,
templates may have a wide variety of origins, e.g., pathological
samples, forensic samples, archaeological samples, etc. Biological
specimens may, for example, include whole blood, lymphatic fluid,
serum, plasma, sweat, tear, saliva, sputum, cerebrospinal (CSF)
fluids, amniotic fluid, seminal fluid, vaginal excretions, serous
fluid, synovial fluid, pericardial fluid, peritoneal fluid, pleural
fluid, transudates, exudates, cystic fluid, bile, urine, gastric
fluids, intestinal fluids, fecal samples, and swabs or washes
(e.g., oral, nasopharangeal, optic, rectal, intestinal, vaginal,
epidermal, etc.) and/or other biological specimens.
[0066] Various sample processing steps may be accomplished to
prepare the nucleic acid template. In some cases, such as
amplification from plasmids or bacteriophages, crude sample will
suffice. In other cases, such as amplification of large fragments
from genomic DNA, highly purified template is preferred. Sample
preparation steps may take place on or off the droplet
microactuator.
[0067] The system of the invention may be configured and programmed
to permit processing of a biological sample to prepare a droplet
including a nucleic acid template for amplification. Some portion
or all of this processing may be effected on or off the droplet
microactuator, e.g., using beads having reagents bound thereto with
affinity for target organisms to isolate the target organisms from
a biological sample. The droplet microactuator may process the
sample by dividing it into one or more discrete droplets for
subsequent operations on the droplet microactuator.
[0068] Specimens may, in some instances, be treated to change
reduce viscosity during subsequent droplet operations. For example,
samples can be prepared on the droplet microactuator or off the
droplet microactuator by mixing with an alkaline solution (for
example, 10% KOH) or reducing agents such as dithiothreitol (DTT)
or dithioerythritol (DTE) to liquefy the sample and render it
sufficiently fluid to facilitate droplet operations on a droplet
microactuator. Other examples of suitable sample preparation
techniques are described in U.S. Patent Application No. 60/745,950,
entitled "Apparatus and Methods of Sample Preparation for a Droplet
Microactuator," filed on Apr. 28, 2006.
[0069] A droplet including the nucleic acid template may be
combined with amplification reagents to provide an
amplification-ready droplet, e.g., combined with PCR reagents to
yield a PCR-ready droplet. Depending on the reagents selected, the
amplification-ready droplet may be isothermally amplified or
thermal cycled to effect amplification of a target nucleic acid.
Amplified product may be detected and/or quantified in real-time on
a droplet microactuator. In this manner, the invention provides
on-chip, real-time, quantitative amplification to detect and
quantify a target nucleic acid in a sample.
[0070] As nearly 100% of the sample can be utilized for analysis
(there is no requirement for priming of channels or pumps), very
small sample volumes (e.g., less than about 100 .mu.L or less than
about 50 .mu.L or less than about 25 .mu.L) can be analyzed. Many
tests can be performed using a single, small sample, and reagent
costs can be minimized.
8.1.2 Reagents
[0071] In the amplification protocols of the invention, various
reagents may be combined with a nucleic acid template to yield an
amplification-ready droplet, such as a PCR-ready droplet. PCR
reagents typically include primers, nucleotides, polymerase, and
buffers. These input reagents may be provided as individual
reagents loaded separately onto the droplet microactuator and
combined using droplet operations on the droplet microactuator.
Moreover, some or all of the reagents may be provided as reagent
mixes that are loaded onto the droplet microactuator in a premixed
form. In one embodiment, all amplification reagents are combined
into a single droplet that must only be combined with a sample
droplet in order to yield an amplification-ready droplet, e.g., a
PCR-ready droplet.
8.1.2.1 Buffer
[0072] Reagents will typically include a buffer. The buffer is
selected to facilitate the amplification reaction. Any buffer which
fulfills this function is suitable. Magnesium ions are usefully
included in the buffer where the nucleic acid being amplified is a
DNA.
[0073] In one embodiment, the buffer includes KCl, Tris and
MgCl.sub.2. Other suitable buffers are described in Chamberlain et
al., Nucleic Acid Research 16:11141-11156 (1988). For example, the
buffer may comprise about 500 mM KCl, about 100 mM Tris-HCl (pH
8.3), and about 15 mM MgCl.sub.2. In another example, the buffer
may comprise about 83 mM (NH.sub.4).sub.2SO.sub.4, about 335 mM
Tris-HCl (pH8.8), about 33.5 mM MgCl.sub.2, about 50 mM
.beta.-Mercapthoethanol, and about 34 mM EDTA. The buffer may also
include primers and/or polymerases.
[0074] In one embodiment, PCR may be performed sequentially or in
parallel in several droplets in which the concentration of one or
more buffer components is systematically varied (e.g., in a series
of droplets) in order to improve or optimize the buffer for a
specific reaction. Thus, for example, any one or more of the
following buffer components may be varied: KCl; Tris; MgCl.sub.2;
(NH.sub.4).sub.2SO.sub.4; .beta.-Mercaptoethanol; EDTA. Once the
best of the tested buffer conditions is identified, PCR can proceed
using the best buffer system or further optimization may be
conducted around the best of the tested buffer systems.
[0075] The invention includes a droplet microactuator including a
droplet thereon which is a buffer or which comprises a buffer
component, as well as systems and/or devices including such a
droplet microactuator, and methods of conducting droplet operations
on or otherwise manipulating such droplet on a droplet
microactuator. Thus, for example, the invention includes a droplet
microactuator comprising a droplet thereon, which droplet comprises
one or more of the following components: KCl, Tris, MgCl.sub.2;
(NH.sub.4).sub.2SO.sub.4; .beta.-Mercapthoethanol; EDTA.
[0076] Further, the invention includes a droplet microactuator
comprising a droplet thereon, which droplet comprises one or more
of the foregoing components at a concentration sufficient to
facilitate amplification of a target nucleic acid. Moreover, the
invention includes such a droplet along with a polymerase,
nucleotides and/or one or more primers at a concentration
sufficient to facilitate amplification of a target nucleic acid.
The invention also includes a method of conducting droplet
operations on or otherwise manipulating any of the droplets
described in this section using the droplet microactuator, device,
and/or system. For example, the droplet operation may include one
of more the following: loading a droplet into the droplet
microactuator; dispensing one or more droplets from a source
droplet; splitting, separating or dividing a droplet into two or
more droplets; transporting a droplet from one location to another
in any direction; merging or combining two or more droplets into a
single droplet; diluting a droplet; mixing a droplet; agitating a
droplet; deforming a droplet; retaining a droplet in position;
incubating a droplet; heating a droplet; vaporizing a droplet;
cooling a droplet; disposing of a droplet; transporting a droplet
out of a droplet microactuator; other droplet operations described
herein; and/or any combination of the foregoing.
8.1.2.2 Primers
[0077] Reagents used in the amplification methods of the invention
will include one or more primers. In typical methods, two primers
are used to define the region of the nucleic acid template that
will be amplified. Primers will typically have a sequence and a
length which is selected to ensure efficient replication with few
mistakes. Such primers are often in the range of about 18-24 bases
long. Other requirements for selection of effective primers are
known. Examples of suitable primer properties include lack of
internal secondary structure, 40-60% G/C content, balanced
distribution of G/C and A/T rich domains, and lack of complementary
at the 3' ends to avoid formation of primer dimers. Though not
specifically required, primers with one or more of these properties
may be suitably employed in the practice of the invention.
Additionally, the melting temperature (Tm) for primers is typically
selected to permit annealing temperatures of about 55 to about
65.degree. C., or about 62 to about 65.degree. C. A variety of
publicly available computer programs exist to help identify primers
with properties suitable for use in amplification settings. Where
two primers are used, they are typically provided in equal
concentrations. Primers may not be necessary in cases in which the
nucleic acid being amplified is an RNA.
[0078] In some embodiments, degenerate mixtures of primers are
used. For example, since a given amino acid sequence may be encoded
by several possible codons, the mixture may include all possible
sequences covering all codon combinations for a target polypeptide.
The degenerate primer mixture may be simplified by identifying
codon bias for the organism in question, and including only primers
commonly used by the organism.
[0079] Primers are provided at any concentration which facilitates
amplification of the target nucleic acid. Concentrations should be
low enough to avoid an undue amount of mispriming, accumulation of
non-specific product, and/or primer-dimer formation. Primer
concentration should be high enough to avoid exhaustion of primer
prior to completion of the amplification reaction. In some
embodiments, concentrations range from about 0.1 .mu.M to about 1
.mu.M or from about 0.1 .mu.M to about 0.6 .mu.M.
[0080] Primers may also be labeled. For example, labels may be
selected to facilitate detection, localization, quantification,
and/or isolation of PCR product. For example, biotinylation can be
used to facilitate detection and/or purification using streptavidin
to capture biotinylated PCR product on surface. Further,
streptavidin can be associated with magnetically responsive beads
for capture of biotinylated PCR product. Digoxigenin can also be
used for detection of PCR product. Primers may, for example, be
labeled at their 5' ends and/or internally, and further, labeled
nucleotides may be incorporated into the PCR product for detection,
localization, quantification, and/or isolation.
[0081] The invention includes a droplet microactuator including a
droplet thereon which includes labeled and/or unlabeled primers
(e.g., at concentrations ranging from about 0.1 .mu.M to about 1
.mu.M or from about 0.1 .mu.M to about 0.6 .mu.M) for amplification
of a target nucleic acid in a concentration sufficient to
facilitate the amplification reaction, as well as systems and/or
devices including such a droplet microactuator, and methods of
conducting droplet operations or otherwise manipulating such
droplet on a droplet microactuator. As another example, the
invention includes a droplet microactuator including a droplet
thereon including labeled and/or unlabeled primers at a low enough
concentration to reduce or eliminate mispriming and accumulation of
non-specific product and a high enough concentration to avoid
exhaustion of primer prior to completion of the amplification
reaction. In yet another example, the invention includes a droplet
microactuator comprising a droplet thereon including labeled and/or
unlabeled primers at a concentration ranging from about 0.1 .mu.M
to about 1 .mu.M or from about 0.1 .mu.M to about 0.6 .mu.M.
Further, the invention includes such a droplet along with a
polymerase, nucleotides and/or buffer components at concentrations
selected to facilitate amplification of a target nucleic acid.
Moreover, the invention includes a method of conducting droplet
operations on or otherwise manipulating any of the droplets
described in this section using the droplet microactuator, device,
and/or system. For example, the droplet operation may include one
of more the following: loading a droplet into the droplet
microactuator; dispensing one or more droplets from a source
droplet; splitting, separating or dividing a droplet into two or
more droplets; transporting a droplet from one location to another
in any direction; merging or combining two or more droplets into a
single droplet; diluting a droplet; mixing a droplet; agitating a
droplet; deforming a droplet; retaining a droplet in position;
incubating a droplet; heating a droplet; vaporizing a droplet;
cooling a droplet; disposing of a droplet; transporting a droplet
out of a droplet microactuator; other droplet operations described
herein; and/or any combination of the foregoing.
8.1.2.3 Nucleotides
[0082] Reagents used in the amplification methods of the invention
will include nucleotides. Stock solutions of dNTPs are commercially
available from a variety of sources. Stock solutions are typically
provided at concentrations of 100-300 mM. Stock solutions can be
diluted prior to introduction to the droplet microactuator and/or
on the droplet microactuator using droplet operations to combine
the stock solutions with one or more buffer solutions. Final
concentrations in the PCR-ready droplet will typically range from
about 50 .mu.mol to about 200 .mu.mol. The four dNTPs are typically
provided in equimolar concentrations.
[0083] A variety of modified nucleotides may be employed in the
practice of the invention. Examples include nucleotides designed to
reduce secondary structure resolution, prevent contamination, as
well as radiolabeled nucleotides, non-radioactive labeled
nucleotides, and nucleotides designed to promote random
mutagenesis. For examples, see McPherson et al., PCR, Taylor and
Francis Group, 2006 (the entire disclosure which is incorporated
herein by reference).
[0084] The invention includes a droplet microactuator including a
droplet thereon which includes nucleotides for amplification of a
target nucleic acid in a concentration sufficient to facilitate the
amplification reaction, as well as systems and/or devices including
such a droplet microactuator, and methods of conducting droplet
operations on or otherwise manipulating such a droplet on a droplet
microactuator. Thus, for example, the invention includes a droplet
microactuator comprising a droplet thereon including one or more
nucleotides in a concentration ranging from about 100 mM to about
300 mM (stock concentration) or from about 50 .mu.mol to about 200
.mu.mol (operating concentration). In another example, the
invention includes a droplet microactuator comprising a droplet
thereon including 1, 2, 3 or 4 nucleotides, each in a concentration
ranging from about 100 mM to about 300 mM or from about 50 .mu.M to
about 200 .mu.M. The system of the invention may be configured and
programmed to execute a protocol for diluting stock nucleotide
concentrations to provide droplets comprising operating nucleotide
concentrations. For example, the system of the invention may be
configured and programmed to execute a protocol diluting stock
nucleotide concentrations ranging from about 100 mM to about 300 mM
to provide operating solutions ranging from about 50 .mu.mol to
about 200 .mu.mol. Further, the invention includes
nucleotide-containing droplets along with polymerase(s), primer(s)
and/or buffer components in concentrations selected to provide
conditions that facilitate amplification of a target nucleic acid.
Moreover, the invention includes a method of conducting droplet
operations on or otherwise manipulating any of the droplets
described in this section using the droplet microactuator, device,
and/or system. For example, the droplet operation may include one
of more the following: loading a droplet into the droplet
microactuator; dispensing one or more droplets from a source
droplet; splitting, separating or dividing a droplet into two or
more droplets; transporting a droplet from one location to another
in any direction; merging or combining two or more droplets into a
single droplet; diluting a droplet; mixing a droplet; agitating a
droplet; deforming a droplet; retaining a droplet in position;
incubating a droplet; heating a droplet; vaporizing a droplet;
cooling a droplet; disposing of a droplet; transporting a droplet
out of a droplet microactuator; other droplet operations described
herein; and/or any combination of the foregoing.
8.1.2.4 PCR Polymerases
[0085] A variety of PCR polymerases may be used in the
droplet-based PCR protocols of the invention. Suitable polymerases
will often have optimal activity at about 75.degree. C. and the
ability to retain that activity after prolonged incubation, e.g.,
at temperatures greater than 95.degree. C. Useful polymerases may,
for example, include DNA-dependent DNA polymerases and/or
RNA-dependent DNA polymerases (reverse transcriptases). Various
thermostable polymerases, such as Taq DNA polymerases, may be used.
Suitable examples include AmpliTaq.RTM., AmpliTaq Gold.RTM., the
Stoffel fragment of AmpliTaq.RTM., and others. Examples of
thermostable polymerases with proofreading capability include
Vent.RTM., Tli, DeepVent.RTM., Pfr, Pwo, UlTma.RTM., Accuzyme.RTM.,
and KOD Hifi, DNA polymerases, as well as various exo.sup.-
versions of the foregoing. Polymerase preparations may in some
cases include dyes for determining or confirming concentrations of
PCR reagents. In some cases, the system is configured and
programmed to detect such dyes and calculate reagent concentrations
based on colorimetric measurements. In some cases, the invention
makes use of droplets including a combination of a thermostable
polymerase (e.g., Taq DNA Polymerase) and a proofreading polymerase
(e.g., Pwo DNA Polymerase).
[0086] The invention includes a droplet microactuator including a
droplet thereon which includes one or more polymerases at
concentrations sufficient to facilitate the amplification reaction,
as well as systems and/or devices including such a droplet
microactuator, and methods of conducting droplet operations or
otherwise manipulating such droplet on a droplet microactuator.
Moreover, the invention includes a method of conducting droplet
operations on or otherwise manipulating any of the droplets
described in this section using the droplet microactuator, device,
and/or system. For example, the droplet operation may include one
of more the following: loading a droplet into the droplet
microactuator; dispensing one or more droplets from a source
droplet; splitting, separating or dividing a droplet into two or
more droplets; transporting a droplet from one location to another
in any direction; merging or combining two or more droplets into a
single droplet; diluting a droplet; mixing a droplet; agitating a
droplet; deforming a droplet; retaining a droplet in position;
incubating a droplet; heating a droplet; vaporizing a droplet;
cooling a droplet; disposing of a droplet; transporting a droplet
out of a droplet microactuator; other droplet operations described
herein; and/or any combination of the foregoing. Further, the
invention includes polymerase-containing droplets on a droplet
microactuator of the invention along with nucleotides, primer
and/or buffer in concentrations selected to provide conditions
sufficient to facilitate amplification of a target nucleic
acid.
8.1.2.5 Detection of Amplified Product
[0087] In some embodiments, amplified nucleic acid will be detected
after some number of amplification cycles. For example, amplified
nucleic acid may be quantified during or after each cycle, or after
some predetermined number of cycles, e.g., after each set of 2, 3,
4, 5, 6, 7, 8, 9, or 10 cycles. Detection generally involves using
droplet operations to transport the droplet into detection zone in
which a sensor measures some aspect of the droplet, such as a
physical, chemical or electrical aspect, which correlates with
amplification. The system may be programmed so that amplification
cycles may be continued until detection reveals that a desired
level of signal has been achieved. In one embodiment, the detection
method for amplification is a fluorescence technique.
[0088] Further, in some embodiments, a droplet comprising amplified
nucleic acid may be transported for further processing/detection.
For example, in diagnostic embodiments, a droplet including
amplified nucleic acid may be transported for detection of the
presence of a target diagnostic nucleic acid. The target nucleic
acid may, for example, include a nucleic acid from the pathogenic
organism, such as a DNA or RNA associated with a parasite,
bacteria, fungus or virus. The droplet microactuator may be
provided as a component of an integrated and portable diagnostic
platform. The system may provide for fully automated, rapid
detection of a panel of infectious diseases by real-time PCR. The
system may be used at the bedside, stat laboratory, physician's
office, or in the field.
[0089] Fluorescence detection is suitable for detection of
amplified nucleic acid. Light emitting diodes (LEDS) and laser
diodes are suitable as excitation sources because of their small
physical size, low power requirements and long life. LEDs are
appealing because of their low cost and laser diodes because of
their narrow spectral width, and the fact that they can be focused
to small spot sizes without discarding a substantial amount of
light.
[0090] In addition to the reagents already discussed, reagents
usefully employed in nucleic acid amplification protocols of the
invention include various detection reagents, such as fluorescent
and non-fluorescent dyes and probes. For example, the protocols may
employ reagents suitable for use in a TaqMan reaction, such as a
TaqMan probe; reagents suitable for use in a SYBR.RTM. Green
reaction, such as SYBR.RTM. Green; reagents suitable for use in a
molecular beacon reaction, such as a molecular beacon probe;
reagents suitable for use in a scorpion reaction, such as a
scorpion probe; reagents suitable for use in a fluorescent
DNA-binding dye-type reaction, such as a fluorescent probe; and/or
reagents for use in a LightUp protocol, such as a LightUp
probe.
[0091] The invention includes a droplet microactuator including a
droplet thereon which includes one or more detection reagents, such
as any one or more of the aforementioned probes, at concentrations
sufficient to facilitate detection of the amplification reaction,
as well as systems and/or devices including such a droplet
microactuator, and methods of conducting droplet operations or
otherwise manipulating such droplet on a droplet microactuator.
Moreover, the invention includes a method of conducting droplet
operations on or otherwise manipulating any of the droplets
described in this section using the droplet microactuator, device,
and/or system. For example, the droplet operation may include one
of more the following: loading a droplet into the droplet
microactuator; dispensing one or more droplets from a source
droplet; splitting, separating or dividing a droplet into two or
more droplets; transporting a droplet from one location to another
in any direction; merging or combining two or more droplets into a
single droplet; diluting a droplet; mixing a droplet; agitating a
droplet; deforming a droplet; retaining a droplet in position;
incubating a droplet; heating a droplet; vaporizing a droplet;
cooling a droplet; disposing of a droplet; transporting a droplet
out of a droplet microactuator; other droplet operations described
herein; and/or any combination of the foregoing. Further, the
invention includes nucleotide-containing droplets on a droplet
microactuator of the invention along with a nucleotides, primer,
detection probe and/or buffer in concentrations selected to provide
conditions sufficient to facilitate amplification of a target
nucleic acid.
[0092] Furthermore, the invention includes methods of detecting
and/or quantifying amplification which methods include measuring a
signal (e.g., a fluorescent signal) from droplet on a droplet
microactuator. Thus, for example, the method may employ exposure of
a droplet potentially including a fluorescent dye (such as
SYBR.RTM. Green) to a light source at a wavelength selected to
cause the compound to fluoresce and measuring the resulting
fluorescence. Fluorescence emitted from the droplet can be tracked
during an amplification reaction to permit monitoring of the
reaction, e.g., using a SYBR.RTM. Green-type compound. A system of
the invention may, for example, be programmed to detect such
fluorescence and to display a corresponding graph or other output
permitting a user to track the progress of a PCR reaction in
real-time.
[0093] In another example, the invention includes a method of
detecting and/or quantifying the presence of a target nucleic acid
by including a probe with specificity for a target nucleic acid
(e.g., a TaqMan-type probe) in an amplification-ready droplet
potentially including the target nucleic acid, thermal cycling the
amplification-ready droplet, and detecting any fluorescence signal
caused by degradation of the probe, where a fluorescent signal is
indicative of the presence of the target nucleic acid in the
droplet. The invention includes corresponding methods using other
target-specific probes, such as scorpion probes and molecular
beacons.
8.1.3 Thermal Cycling
[0094] In the practice of the invention, a PCR-ready droplet is
thermal cycled in order to effect an amplification of a target
nucleic acid. Tight control of thermal cycling may be necessary for
effective amplification of certain nucleic acids. Examples of
structures designed to provide controlled thermal cycling on a
droplet microactuator are discussed in Section 8.8.6 below.
Typically, each thermal cycle will involve at least two steps:
[0095] (1) heating the droplet to a temperature sufficient to
denature double stranded nucleic acid in the droplet into
single-stranded DNA (typically about 90-100.degree. C.); and [0096]
(2) lowering the droplet temperature to permit primers to anneal to
their complementary sequences on the nucleic acid template strands
(typically about 50-75.degree. C.).
[0097] In some cases a thermal cycle may also involve a third step:
[0098] (3) adjusting the droplet temperature to facilitate
extension of the double stranded segment of the nucleic acid to be
extended by incorporation of additional nucleotides (typically
about 70-75.degree. C.).
[0099] Depending on the reagents selected, incorporation of
additional nucleotides may be accomplished at the same temperature
at which the primers are permitted to anneal to the nucleic acid
template strands, and thus the temperature adjustment of the third
step may not be necessary. Additional thermal cycling steps may
also be incorporated in various protocols of the invention.
[0100] The invention permits multiple droplets to be thermal cycled
in parallel. Thus, in various embodiments, more than 2, 3, 4, 5,
10, 20, 30, 40, 50, 100, or 1000 amplification-ready droplets are
thermal cycled in parallel on a single droplet microactuator. In
some embodiments, detection of amplification in these droplets is
measured in parallel in real time.
[0101] In one embodiment, each droplet undergoing thermal cycling
is positioned in proximity to a sensor, or is transported into
proximity with a sensor, so that a signal from the droplet
correlating with amplification can be monitored in real time. The
system may output real-time information accessible to a user which
is indicative of the progress of the amplification process.
Further, the system may be arranged to permit such output when
thermal cycling multiple droplets in parallel, e.g., more than 2,
3, 4, 5, 10, 20, 30, 40, 50, 100, or 1000 amplification-ready
droplets are thermal cycled in parallel on a single droplet
microactuator and the system outputs real-time information is
indicative of the progress of the amplification process
[0102] The methods of the invention may include a temperature
optimization step or protocol for optimizing temperatures and/or
times for denaturation, annealing, and/or extension. In this step,
one or more heating zones is used to vary the temperature of one of
more heating steps. For example, the methods may include an
optimization step or protocol for optimization of annealing
temperature. A series of droplets may be thermal cycled using
varied annealing temperatures followed by detection to quantify
amplification and thereby determine which of the tested annealing
temperatures produces the best results. Subsequent thermal cycling
can be conducted at the selected temperature. Similarly a series of
droplets may be cycled through annealing temperatures for different
periods of time followed by detection to quantify amplification and
thereby determine which of the tested time periods produces the
best results at a given temperature. Subsequent thermal cycling can
be conducted using the selected time period. Further, such
optimization protocols can be executed sequentially or
simultaneously in order to determine both the optimum temperature
and the optimum time period. Similar protocols may be executed for
optimizing temperatures and/or time periods for denaturation and/or
extension steps.
[0103] In one embodiment, thermal cycling is accomplished by
heating and cooling the entire droplet microactuator. This
embodiment generally involves the following steps: [0104] (1)
heating the droplet microactuator to a temperature sufficient to
denature the double-stranded DNA (present in a droplet on the
droplet microactuator) into single-stranded DNA; [0105] (2)
lowering the temperature of the droplet microactuator to a
temperature sufficient to permit primers (present in a droplet on
the droplet microactuator) to anneal to their complementary
sequences on the nucleic acid template strands; [0106] (3)
optionally, adjusting the temperature of the droplet microactuator
to facilitate extension of the double stranded segment of the
nucleic acid (present in a droplet on the droplet microactuator) by
incorporation of additional nucleotides.
[0107] The thermal cycling protocols of the invention may be
conducted without significant loss of water or other components of
the PCR-ready droplet. Further, the thermal cycling protocols may
be conducted without significant cross-contamination between
droplets. Moreover, the thermal cycling may be conducted without
significant disruption in the capability of the droplet
microactuator to continue conducting droplet operations. For
example, droplet operations may in some cases continue to be
conducted at the various denaturation, annealing, and/or extension
temperatures.
[0108] In a related embodiment, thermal cycling is accomplished by
heating and cooling a section or region of the droplet
microactuator. This approach generally involves the following
steps: [0109] (1) heating a section or region of the droplet
microactuator to a temperature sufficient to denature the
double-stranded DNA (present in a droplet on the droplet
microactuator) into single-stranded DNA; [0110] (2) lowering the
temperature of a section or region of the droplet microactuator to
a temperature sufficient to permit primers (present in a droplet on
the droplet microactuator) to anneal to their complementary
sequences on the nucleic acid template strands; [0111] (3)
optionally, adjusting the temperature of a section or region of the
droplet microactuator to facilitate extension of the double
stranded segment of the nucleic acid (present in a droplet on the
droplet microactuator) by incorporation of additional
nucleotides.
[0112] In one embodiment, this approach is conducted using a
droplet microactuator with a single integrated heater 202, as
illustrated in FIG. 2A.
[0113] In another embodiment, regions of the droplet microactuator
may be maintained at the required temperatures, and the droplets
may be transported through the appropriate temperature regions in
order to accomplish the thermal cycling. This approach generally
involves the following steps: [0114] (1) transporting an
amplification-ready droplet to a region of the droplet
microactuator that is maintained at a temperature appropriate to
cause denaturation of double-stranded DNA in the droplet into
single-stranded DNA; [0115] (2) transporting the
amplification-ready droplet to a region of the droplet
microactuator that is maintained at a temperature sufficient to
permit primers in the droplet to anneal to their complementary
sequences on the nucleic acid template strands; and [0116] (3)
optionally, transporting an amplification-ready droplet to a region
of the droplet microactuator that is maintained at a temperature
sufficient to facilitate or optimize extension of the
double-stranded segment of the nucleic acid in the droplet by
incorporation of additional nucleotides.
[0117] In this embodiment, thermal cycling is accomplished by
repeating the transporting steps to move the droplets from zone to
zone. In one embodiment, the droplet microactuator includes only
one thermal zone for each required temperature, and thermal cycling
is accomplished by rotating each droplet through the appropriate
thermal zones. In another embodiment, the droplet microactuator
includes two or more of each of the thermal zones. In yet another
embodiment, the droplet microactuator includes two or more of one
or more of the thermal zones. Further, the droplet microactuator
may include 2, 3 or more thermal zones, each of which may be heated
to a different specified temperature. In one embodiment, this
approach is conducted using a droplet microactuator with a
plurality of integrated heaters 204, as illustrated in FIG. 2B.
[0118] Further, one or more heaters may be used to establish a
continuous thermal gradient across a region of the droplet
microactuator. In this embodiment, an electrode matrix, electrode
path or series of electrode paths may be employed to locate the
droplet in the appropriate temperature zone to effect the required
thermal cycling steps. Thermal cycling may thus be accomplished by
transporting the droplet to an electrode at the appropriate
position within the thermal gradient to achieve the target
temperature. Variations in temperature, e.g., to optimize any of
the various denaturing, annealing and/or extension steps, may be
effected by simply varying the location of the droplet within the
thermal zone.
[0119] Thermal cycling may involve the use of various heating
and/or cooling modalities to establish target temperature zones for
denaturation, annealing and/or extension. These heating and cooling
modalities may be arranged to facilitate a suitable temperature
ramp between the target temperature zones. The ramp may be
controlled by changing the temperature of a specific heating and/or
cooling modality and/or by selecting heating and cooling modalities
at distances selected to effect target temperature zones with
suitable temperature ramps. The droplet microactuator may have
heating and/or cooling modalities with temperature ranges and
spacing selected to create a predetermined set of potential target
temperature zones and temperature ramps. Various heating and/or
cooling modalities may be included between target temperature zones
to adjust the ramp between zones.
[0120] In one embodiment, the droplet microactuator includes a
series of independently adjustable heating elements. The
temperature of each heating element may be adjusted to provide for
an appropriate heating ramp as droplets pass from one target
temperature zone to the next. Further, distance between heating
elements at target temperatures may be selected to facilitate an
appropriate temperature ramp and/or to prevent overheating caused
by interaction between closely situated heating elements. Such
approaches provide flexibility in working with a variety of
protocols each requiring different target temperature zones and
ramp profiles. For example, in a series or matrix of heating
elements, target temperature zones may be at adjacent heating
elements and/or may be separated by one or more heating elements
such that they are separated by a greater distance. In this way,
distances may be varied to account for temperature requirements of
a variety of protocol requirements. A system of the invention may
select optimal heating elements for establishing target temperature
zones with appropriate or optimal temperature ramps between the
heating zones.
[0121] The methods of the invention may include a temperature
optimization step or protocol for optimizing temperatures and/or
times for the denaturation, annealing, and/or extension phases of
the thermal cycle. As an example, the methods may include an
optimization step or protocol for optimization of annealing
temperature. A series of heating zones may be established in which
amplification-ready droplets are cycled through different annealing
temperatures to determine which annealing temperature produces
optimum results. Subsequent thermal cycling can be conducted at the
optimum temperature. Similarly a series of amplification-ready
droplets may be cycled using a protocol in which the time of the
annealing phase is systematically varied to determine which time
period produces optimum results at a given temperature. Subsequent
thermal cycling can be conducted using the optimum time period.
Further, such protocols can be executed sequentially or
simultaneously in order to determine both the optimum temperature
and the optimum time period. Similar protocols may be executed for
optimizing denaturation and/or extension steps. Optimization
protocols my run sequentially or in parallel.
[0122] Similarly, the methods of the invention may include a
temperature optimization step or protocol using multiple
independently heated thermal zones for optimizing temperatures
and/or times for denaturation, annealing, and/or extension. For
example, a series of heating zones may be established through which
amplification-ready droplets are transported. The zones may include
temperatures targeted to promote denaturation, annealing, and/or
extension. In a specific droplet set, the temperature of one of the
denaturation, annealing and/or extension zones may be
systematically varied for a set of PCR-ready droplets, while the
other two temperatures remain constant. Multiple droplet sets can
be tested so that each of the temperature parameters may be varied
as needed. One or more of the multiple droplet sets may be tested
sequentially and/or in parallel. Variations in heating zone
temperature may, for example, be controlled by the processor (e.g.,
controlling the temperature of a heating element and/or controlling
a location of a droplet within a heating gradient) via software
pre-programmed to execute an optimization protocol and/or via
software controlled by a user via a user interface. The timing of
each of the phases of the thermal cycle may be optimized in like
manner. Optimization protocols my run sequentially or in
parallel.
[0123] Moreover, the invention includes a method of conducting one
or more droplet operations using a PCR-ready droplet on a droplet
microactuator at an elevated temperature, e.g., at a temperature
which is greater than about 70, 75, 80, 85, 90, 95, or 100.degree.
C. For example, the droplet operation may include: loading a
droplet into the droplet microactuator; dispensing one or more
droplets from a source droplet; splitting, separating or dividing a
droplet into two or more droplets; transporting a droplet from one
location to another in any direction; merging or combining two or
more droplets into a single droplet; diluting a droplet; mixing a
droplet; agitating a droplet; deforming a droplet; retaining a
droplet in position; incubating a droplet; heating a droplet;
vaporizing a droplet; cooling a droplet; disposing of a droplet;
transporting a droplet out of a droplet microactuator; other
droplet operations described herein; and/or any combination of the
foregoing. Still further, the invention includes a method of
heating and/or cooling a droplet by transporting the droplet
between two or more temperature zones on a droplet microactuator.
Further, the invention includes a method of heating and/or cooling
a droplet by transporting the droplet between two or more
temperature zones on a droplet microactuator when the temperature
zones range from about 40.degree. C. to about 120.degree. C. The
invention also includes a method of heating and/or cooling a
droplet by transporting the droplet between two or more temperature
zones on a droplet microactuator when the temperature zones range
from about 40.degree. C. to about 120.degree. C. to achieve target
temperatures at least some of which are at a temperature which is
greater than about 70, 75, 80, 85, 90, 95, or 100.degree. C.
[0124] The invention includes a droplet microactuator or droplet
microactuator system having one or more input reservoirs loaded
with reagents for conducting biochemical reactions, such as the
reagents described for use in nucleic acid amplification protocols,
affinity-based assay protocols, sequencing protocols, and protocols
for analyses of biological fluids. For example, one or more
reservoirs may include reagents for providing buffer, primers,
nucleotides, polymerases, and other reagents for conducting a PCR
reaction. In one embodiment, one or more reservoirs includes a
buffer which includes two or more reagents for conducting a PCR
reaction, where in the reagents are selected from primers,
nucleotides, polymerases, and other PCR reagents. In another
embodiment, one or more of the reservoirs includes a droplet
including all reagents required for conducting a PCR reaction, such
that when combined with a sample droplet including a nucleic acid
template, the result is a droplet which is ready for PCR thermal
cycling. The invention also includes a droplet microactuator or
droplet microactuator system, having one or more input reservoirs
loaded with a sample for conducting a PCR reaction.
8.1.4 Amplification Protocols
[0125] It will be appreciated by one of skill in the art in light
of the present disclosure that many variations are possible within
the scope of the invention. In general, the protocols involve
combining two or more droplets comprising PCR reagents and template
to yield a PCR-ready droplet, and thermal cycling the PCR-ready
droplet at temperatures selected to facilitate amplification of a
target nucleic acid.
[0126] Upstream, the protocol may involve various sample processing
steps in order to provide a nucleic acid template that is ready for
PCR amplification. For example, reverse transcription of RNA may be
used prior to PCR to provide a stable DNA nucleic acid template for
amplification. Thus, in one embodiment, the invention provides a
method of preparing a droplet comprising a DNA nucleic acid
template, wherein the method includes performing droplet-based
reverse transcription of RNA to yield the nucleic acid
template.
[0127] A "Hot Start" approach can be used to minimize the formation
of primer-dimers during reaction preparation. By limiting
polymerase activity prior to PCR cycling, non-specific
amplification is reduced and target yield is increased. Common
methods for Hot Start PCR include chemical modifications,
wax-barrier methods, and inhibition by a Taq-directed antibody.
[0128] Downstream, the protocol may involve various subsequent
steps, such as sequencing of an amplified nucleic acid, e.g., using
a pyrosequencing approach or separation of amplified fragments
using capillary electrophoresis,
[0129] Various specialized techniques may also be used during the
PCR process. For example, primers with sequences not completely
complementary to the nucleic acid template can be used for
droplet-based in vitro mutagenesis. Thus, for example, the
invention may include a method of accomplishing in vitro
mutagenesis in a droplet on a droplet microactuator, when the
method involves combining two or more droplets including PCR
reagents and primers selected for mutagenesis in quantities
sufficient to facilitate amplification of a mutated version of the
target nucleic acid. Further, the mutated version of the target
nucleic acid may be transported for downstream processing, e.g.,
sequencing of the mutated version of the target nucleic acid to
confirm the desired mutation.
[0130] In a medical diagnostic aspect of the invention, molecular
tags, such as digoxigenin (DIG) or biotin-labeled dUTP can be used
to permit detection of specific sequences. The labeled PCR products
may, for example, be used as hybridization probes or detected by
use of capture probes.
[0131] In many protocols, it will be desirable to simultaneously
process one or more control droplets to determine the quality or
fidelity of the reaction. Thus, for example, in order to ensure
that contamination has not occurred one or more PCR-ready droplets
without the sample template may be thermal cycled and otherwise
processed in the same manner as droplets including the sample
template. Detection of amplified nucleic acid in the control
droplets would be indicative of contamination. Other control
droplets may include known quantities or concentrations of template
material, or known quantities or concentrations of fluorescent dye.
Control droplets may be processed on the same droplet microactuator
as the sample droplets, simultaneously with, before and/or after,
processing of the actual sample droplet.
[0132] The system provides the possibility of independent
software-based customization of reaction protocols and conditions
for each sample or assay. This, combined with the scalability of
the platform ensures that the capabilities of the system can be
extended to include a wide range of nucleic acid targets.
[0133] The invention includes methods of conducting droplet
operations on amplification reagents. For example, the invention
includes a method of conducting one or more droplet operations on a
droplet including buffer, primers, nucleotides, polymerases, and/or
other PCR reagents.
[0134] The invention also includes a method of conducting one or
more droplet operations using a buffer droplet on a droplet
microactuator including one or more primers. The invention also
includes a method of conducting one or more droplet operations
using a buffer droplet on a droplet microactuator including one or
more nucleotides. The invention also includes a method of
conducting one or more droplet operations using a buffer droplet on
a droplet microactuator including one or more polymerases, e.g.,
DNA polymerases. The invention also includes a method of conducting
one or more droplet operations using a buffer droplet on a droplet
microactuator including one of more reverse transcriptases. In
another embodiment, the invention includes a method of conducting
one or more droplet operations using a buffer droplet on a droplet
microactuator which includes 2, 3, 4 or more PCR reagents selected
from the categories including primers, nucleotides, polymerases,
and other PCR reagents. Further, the invention includes a method of
conducting one or more droplet operations using a PCR-ready droplet
including one or more buffers, primers, nucleotides, polymerases,
and nucleic acid templates including a target nucleic acid
sequence.
[0135] The droplet-based amplification protocols are also useful
for analyzing RNA content. In some embodiments, RNA will be the
initial target nucleic acid. A two buffer system may be used to
provide one buffer for the reverse transcription (RT) step that
creates cDNA from the viral RNA, and a different buffer selected to
facilitate the DNA amplification step. In a related embodiment, a
single buffer method is used in which a buffer is provided that is
compatible for both reactions but not necessarily optimal for
either.
[0136] In one embodiment, a droplet-based PCR can be executed on a
droplet microactuator to quantitate the changes in gene expression
levels for relevant cancer biomarkers, e.g., vascular endothelial
growth factor (VEGF) and the cyclin-dependent kinase inhibitors
p21(Cip1) and p27(Kip1). For example, cells in a droplet, whether
suspended or bound to a surface, can be lysed. Freed poly(A) mRNA
can be captured in droplets using beads, such as oligo (dT)
magnetically responsive beads. Reagents are available from Dynal
Biotech in its mRNA DIRECT Micro Kit. Mixing or agitation of
droplets may be used to enhance cell lysis and enhance capture of
poly (A) mRNA onto beads. mRNA from oligo (dT) magnetically
responsive beads can be eluted by thermally melting the RNA-DNA
duplex. The appropriate temperature depends on the length of the
strand. Beads can be washed using droplet-based washing protocols
as described elsewhere herein. PCR (e.g., qRT-PCR) can be performed
using a droplet-based protocol on the droplet microactuator with
the appropriate primers for the gene targets (e.g., VEGF, p21(Cip1)
and p27(Kip1)). Droplet-based RNA amplification may also be
accomplished using the Van Gelder and Eberwine technique.
[0137] The invention provides droplet-based rolling circle
amplification for DNA. In the rolling circle approach, a buffer
droplet including a dsDNA his heated on a droplet microactuator to
a temperature sufficient to result in denaturation of the dsDNA
(typically about 95.degree. C.). Incubation time may in some
instances range from about 1 to about 10 minutes. A droplet
including a circularizable probe is combined with the droplet
including the denatured DNA to anneal and ligate the circularizable
probe to the target dsDNA at an effective temperature (e.g., about
60.degree. C.) in buffer with a polymerase (e.g., T. flavus DNA
polymerase) and an appropriate ligase (e.g., Ampligase DNA ligase).
Incubation may in some cases be less than about 45 minutes. The
resulting droplet is combined with rolling circle primer, buffer,
O29 DNA polymerase, at a decreased temperature (e.g., about
31.degree. C.). Incubation time may in some cases range from about
2 to about 30 minutes. Biotin may be incorporated with the O29 DNA
polymerase to capture the amplicon on a streptavidin bead or
surface and visualized with a fluorescent probe.
[0138] The invention provides droplet-based strand displacement
amplification (SDA) for DNA. In this embodiment, a buffer droplet
including a dsDNA fragment with target specific amplification
primers is heated on a droplet microactuator to a temperature
sufficient to result in denaturation of the dsDNA (typically about
95.degree. C.). Incubation time may in some instances be for less
than about 4 minutes. The droplet is then cooled to an annealing
temperature (e.g., about 37.degree. C.) to result in annealing.
Annealing time may in some cases be for less than about 4 minutes.
The droplet is combined using droplet operations with a droplet
including a restriction endonuclease and exo(minus) Klenow
polymerase. The resulting droplet is isothermally incubated on the
droplet microactuator at a temperature sufficient to result in DNA
amplification (e.g., about 37.degree. C.). Incubation time may in
some cases be from about 1 to about 5 hours. Amplification can be
detected using, for example, a fluorescent probe or a strand
specific molecular beacon
[0139] The invention provides droplet-based transcription mediated
amplification or NASBA for RNA. In this embodiment, a droplet
including a target nucleic acid is heated on the droplet
microactuator to a temperature sufficient to denature the target
(e.g., about 95.degree. C.). Denaturation time may in some cases be
less than about 4, 3, or 2 minutes. The droplet is then cooled to
an appropriate temperature (e.g., about 41.degree. C.), and
combined using droplet operations with a droplet including add T7
RNA polymerase promoter-target primer 1 and target primer 2. The
resulting droplet is combined using droplet operations with a
droplet including reverse transcriptase, RNAse H and T RNA
polymerase. The droplet temperature is then adjusted to a
temperature sufficient to result in amplification of RNA amplicons.
Amplification time may in some cases last for about 60 minutes.
[0140] One aspect of the invention is a droplet microactuator
having a substrate for immobilization of a nucleic acid. In one
aspect, the substrate is a gold substrate. Another aspect is a
droplet microactuator including a substrate for immobilization of a
nucleic acid and reagents for immobilizing the nucleic acid to the
substrate. Yet another aspect is a droplet microactuator including
a substrate for immobilization of a nucleic acid, reagents for
immobilizing the nucleic acid to the substrate, and a nucleic acid
sample. These reagents and samples, may for example, be stored in
reservoirs on the droplet microactuator and/or in reservoirs or
other containers off the droplet microactuator (e.g., in a
cartridge). In yet another aspect, the invention involves a method
of immobilizing a nucleic acid sample on a substrate comprising
executing droplet operations to bring a droplet comprising the
nucleic acid sample into contact with the substrate and thereby
deposit in the nucleic acid sample on the substrate.
8.1.5 Downstream Analysis
[0141] In some embodiments, a droplet comprising amplified target
nucleic acid may be transported downstream for further analysis.
For example, the droplet may be transported and stream for analysis
by micro gel electrophoresis. The micro gel electrophoresis may
take place on or off the droplet microactuator.
[0142] In one embodiment, a two dimensional micro gel
electrophoresis device, such as the device described by Mohanty et
al. and the American Electrophoresis Society Annual Meeting (see
http://aiche.confex.com/aiche/2005/techprogram/P30621.HTM).
[0143] In some embodiments, droplets including amplified nucleic
acids are contacted with droplets including reagents sufficient to
clone the amplified nucleic acids into suitable vectors. Vectors
may be selected, for example, for use in gene libraries, and/or
expression in cells.
8.2 Nucleic Acid Sequence Analysis
[0144] The invention provides methods, devices and systems for
droplet-based nucleic acid sequence analysis on a droplet
microactuator system which, among other things, avoids problems
associated with the increasingly complex mixtures required by the
approaches of the prior art.
[0145] FIG. 3 illustrates an illustrative droplet microactuator 300
suitable for nucleic acid sequence analysis. In this embodiment,
multiple fluid ports or reservoirs may be provided such as DNA
input reservoir 302, DNA reagents reservoir 304, primer set
reservoirs 306, nucleotide (e.g., dA, dC, dG, and dT) reservoirs
308, and pyrosequencing primer reservoir 310. Wash buffer reservoir
312 may also be provided, as well as waste area 314, thermal
cycling area 316, and imaging area 318. Various thermal cycling
area embodiments may employ a variety of heater configurations such
as those described elsewhere herein. Imaging area 318 may utilize,
for example, a photomultiplier tube (PMT).
[0146] FIGS. 4 and 5 illustrate reaction steps and droplet
operations of an illustrative embodiment of the invention. A
nucleic acid sample may be amplified as needed (on or off the
droplet microactuator) to obtain a sufficient concentration of
nucleic acid for analysis. The nucleic acid sample may be
introduced to a droplet microactuator where it is immobilized on a
solid support. Reagents for denaturing the nucleic acid to single
strand, priming and stepwise extension of the double stranded
portion, may be transported to the immobilized nucleic acid using
droplet microactuation techniques. Importantly, droplets including
reaction products may be transported away from the immobilized
nucleic acid, e.g., for further processing, analysis, and/or waste
disposal. Importantly, detection may in some embodiments be
conducted separately in time and space relative to the extension
synthesis reactions. Among other things, this capability reduces or
eliminates the build-up of certain degradation byproducts caused by
existing methods. A further advantage of the invention is that
detection can occur in proximity to a sensor to improve the
efficiency of light collection and thus the sensitivity of the
analysis.
[0147] The invention may include a droplet microactuator or droplet
microactuator system having one or more input reservoirs loaded
with reagents for conducting sequencing protocols. For example, one
or more reservoirs may include reagents for conducting a
pyrosequencing protocol. The invention also may include a droplet
microactuator or droplet microactuator system, having one or more
input reservoirs loaded with a sample for conducting a
pyrosequencing protocol.
[0148] It will be appreciated that an important aspect of the
invention involves the ability to conduct droplet operations using
each of the sequence analysis reagents and/or samples on a droplet
microactuator. For example, the invention may include: [0149] (1) a
droplet microactuator comprising thereon a droplet comprising any
one or more of the reagents and/or samples described herein for
conducting sequence analyses; [0150] (2) a device or system of the
invention comprising such droplet microactuator; [0151] (3) a
method of conducting droplet operations on or otherwise
manipulating a droplet making use of such droplet microactuator or
system; and/or [0152] (4) a method of conducting an droplet-based
sequence analysis protocol making use of such droplet microactuator
or system.
[0153] For example, the droplet operations may include one or more
of the following: loading a droplet into the droplet microactuator;
dispensing one or more droplets from a source droplet; splitting,
separating or dividing a droplet into two or more droplets;
transporting a droplet from one location to another in any
direction; merging or combining two or more droplets into a single
droplet; diluting a droplet; mixing a droplet; agitating a droplet;
deforming a droplet; retaining a droplet in position; incubating a
droplet; heating a droplet; vaporizing a droplet; cooling a
droplet; disposing of a droplet; transporting a droplet out of a
droplet microactuator; other droplet operations described herein;
and/or any combination of the foregoing. Various other methods,
devices, systems, and other aspects of the invention will be
apparent from the ensuing discussion.
8.2.1 Sample Amplification
[0154] Nucleic acid sequence analysis typically begins with a
sample including an amplified nucleic acid analyte or with a sample
that includes a nucleic acid analyte for amplification. For the
latter, amplification can be performed using standard techniques
and/or using droplet-based amplification on a droplet microactuator
as described in Section 8.1. Amplification may be conducted on the
same droplet microactuator used to conduct sequence analysis
protocols and/or on a separate droplet microactuator. In some
embodiments, a second droplet microactuator and is coupled in fluid
communication with a sequence analysis droplet microactuator.
8.2.2 Nucleic Acid Immobilization
[0155] As illustrated in FIG. 4, the amplified nucleic acid sample
may be immobilized within the droplet microactuator so that reagent
droplets may be brought into contact with the immobilized nucleic
acid. Immobilization may be on a surface of the droplet
microactuator or on other surfaces within the microactuator, such
as beads made from polymers, polymeric resins, and optionally
including magnetically responsive materials.
[0156] Useful substrates for such attachment include glass, gold,
polyacrylamide gels, polypyrrole, Teflon, and optical fibers.
Materials may, for example, be provided as films, particles,
matrices or beads. In one embodiment, the substrate includes
magnetically responsive beads. The droplet microactuator can
include a magnet or electromagnet for producing a magnetic field to
manipulate (e.g., immobilize, release, or move) the magnetically
responsive beads. For example, magnetically responsive beads can be
agitated and immobilized on the microactuator using a magnetic
field to enhance washing steps (see Section 8.6).
[0157] A wide variety of techniques may be used to immobilize
molecules, such as DNA, to surfaces. Examples include those
chemistries used to attach oligonucleotides to the surface of
microarrays and chemistries used in solid phase synthesis
techniques.
[0158] Nucleic acid samples may be thiolated and adsorbed to a gold
substrate. Nucleic acids maybe thiolated, for example, by
substituting a non-bridging internucleotide oxygen of a
phosphodiester moiety with sulfur, e.g., as described in U.S. Pat.
No. 5,472,881, by Beebe et al., entitled "Thiol Labeling of DNA for
Attachment to Gold Surfaces," the entire disclosure of which is
incorporated herein by reference. One or more droplets including
the thiolated nucleic acid can be transported on the droplet
microactuator to a gold surface where the thiolated nucleic acid
sample will be deposited on the gold surface. The droplet including
the thiolated DNA is brought into contact with the gold surface for
a sufficient time for covalent bonds to form between the sulfur and
the gold. Electroactuation techniques may be employed to increase
the surface area of the droplet with the gold surface.
[0159] DNA sample can be biotinylated at the 5'-ends using a water
soluble biotin ester or using a biotinyl phosphoramidite reagent.
Biotinylated DNA can be captured on streptavidin coated substrates.
Thus, a droplet including biotinylated DNA sample can be
transported into contact with the streptavidin surface where the
DNA will be captured and immobilized.
[0160] Chemistry has been described for immobilization of single
stranded DNA on a substrate (S. Taira et al., "Immobilization of
single-stranded DNA by self-assembled polymer on gold substrate for
a DNA chip," Biotechnol Bioeng. 2005 Mar. 30; 89(7):835-8). In this
approach, thioctic acid (TA) is covalently attached to
poly(allylamine hydrochloride) (PAH) in sidechains to immobilize
the polymer on a gold surface by self-assembly.
N-hydroxysuccinimide-ester terminated probe single-stranded (ss)
DNA is easily covalently immobilized onto a TA-PAH-coated gold
surface. The surface may be covered with polyacrylic acid, which
forms ion complexes with the TA-PAH, to reduce the cationic
charge.
[0161] As illustrated in step 3 of FIG. 4, double stranded nucleic
acid is treated with a denaturing reagent, such as NaOH solution,
in order to yield single stranded sample. This step is illustrated
as occurring after the immobilization step; however, it will be
appreciated that denaturation may be effected by transporting a
denaturing reagent into contact with the double stranded nucleic
acid sample, before, during or after immobilization. Denaturation
may also be performed by heating the sample to thermally melt the
double-stranded complex.
[0162] One aspect of the invention is a droplet microactuator
having a substrate for immobilization of a nucleic acid. Another
aspect is a droplet microactuator including a substrate for
immobilization of a nucleic acid and reagents for immobilizing the
nucleic acid to the substrate. Yet another aspect is a droplet
microactuator including a substrate for immobilization of a nucleic
acid, reagents for immobilizing the nucleic acid to the substrate,
and a nucleic acid sample. These reagents and samples, may for
example, be stored in reservoirs on the droplet microactuator
and/or in reservoirs or other containers off the droplet
microactuator (e.g., in a cartridge). In one embodiment of a
reservoir loading assembly, reagent and/or sample reservoirs (e.g.,
in vials or syringes) may be coupled in fluid communication with
droplet microactuator reservoirs so that fluid from the vials may
flow or be forced directly into the droplet microactuator
reservoirs. This aspect of the invention is scalable, such that the
number of reservoirs and reservoir loading assemblies may be
increased as needed to include slots for as many reagents as
required to conduct a desired protocol. Reagent/sample reservoirs
and reagent/sample loading are discussed further in Sections 8.8.4
and 8.8.5.1.
8.2.3 Polymerase Facilitated Nucleotide Incorporation
[0163] As illustrated in steps 4 and 5 of FIG. 4, the immobilized,
single stranded nucleotide sample is primed to yield a double
stranded segment. Priming may, for example, be achieved by
transporting a droplet comprising primer into contact with the
immobilized sample.
[0164] The primed sample is reacted with a deoxynucleotide
triphosphate (dNTP) in the presence of a polymerase. This reaction
may be achieved by transporting one or more droplets including a
deoxynucleotide triphosphate (dNTP) and a polymerase into contact
with the immobilized sample. If the dNTP is complementary to the
first base in the single stranded portion of the nucleic acid
sample, the polymerase catalyzes its incorporation into the DNA
strand. Each incorporation event is accompanied by release of
pyrophosphate (PPi) in a quantity corresponding to the quantity of
incorporated nucleotide. Incorporation events can thus be
determined by measuring the PPi released. Addition of dNTPs is
typically performed one at a time, each in a separate buffer.
Nucleotide incorporation proceeds sequentially along each
immobilized template as each nucleotide is made available in a
preselected or programmed order.
[0165] A variety of native and modified polymerases may be used.
Modified polymerases include, for example, native sequences with
additions, insertions or replacements, that result in a polymerase
that retains the capacity to facilitate incorporation of a
nucleotide into a primed sample. The polymerase may be an
exonuclease deficient polymerase. The large or Klenow fragment of
DNA polymerase may also be used.
[0166] A dATP or ddATP analogue may be selected which does not
interfere in the enzymatic PPi detection reaction but which
nonetheless may be incorporated by a polymerase into a growing DNA
chain without interfering with proper base pairing. Examples of
suitable analogues include [1-thio]triphosphate (or
.alpha.-thiotriphosphate) analogues of deoxy or dideoxy ATP, e.g.,
deoxyadenosine [1-thio]triphospate, or deoxyadenosine
.alpha.-thiotriphosphate (dATPaS) as it is also known. These and
other analogues are described in U.S. Pat. No. 6,210,891, by Nyren,
et al., entitled "Method of sequencing DNA," the entire disclosure
of which is incorporated herein by reference for its teaching
concerning such analogues.
[0167] Single stranded binding protein may be included to extend
the length of sequences that may be sequenced by reducing folding
of the single stranded sample. Thus, for example, the invention
includes a droplet microactuator including a droplet including
single stranded binding protein. The droplet may be an
amplification-ready droplet including single stranded binding
protein. The invention includes methods of conducting droplet
operations on a droplet including single stranded binding
protein.
8.2.4 Detection of Nucleotide Incorporation
[0168] Determination of whether a specific base has incorporated at
the target site may involve quantification of PPi released during
the incorporation reaction. As each dNTP is added to a growing
nucleic acid strand during a polymerase reaction, a PPi is
released. PPi released under these conditions can be detected
enzymatically e.g. by the generation of light in the
luciferase-luciferin reaction (discussed further below). As the
process continues, the complementary strand is assembled, and the
nucleotide sequence is determined from the signal peaks. The system
may produce a program, as illustrated in FIG. 5.
8.2.4.1 Conversion of PPi to ATP
[0169] In some cases, PPi released during an incorporation event
may be detected indirectly. PPi quantification may, for example, be
accomplished by quantifying ATP produced from APS in the presence
of an enzymatic catalyst. ATP sulfurylase quantitatively converts
PPi to ATP in the presence of adenosine 5' phosphosulfate (APS).
Thus, in one embodiment, PPi can be converted to ATP, and the
quantity of ATP can be measured to determine the quantity of dNTP
incorporated during the reaction.
8.2.4.2 Quantification of ATP
[0170] Once PPi is converted to ATP, the ATP can be quantified to
measure the incorporation of dNTP. As illustrated in FIG. 5, ATP
drives the luciferase-mediated conversion of luciferin to
oxyluciferin that generates visible light in quantities that are
proportional to the quantity of ATP. The light produced in the
luciferase-catalyzed reaction may be detected, e.g., by a charge
coupled device (CCD) camera, photodiode and/or photomultiplier tube
(PMT). Light signals are proportional to the number of nucleotides
incorporated. Detected signal can be translated into a system
output corresponding to the results which is viewable by a
user.
[0171] Luciferin-luciferase reactions to detect the release of PPi
have been described. For example, a method for continuous
monitoring of PPi release based on the enzymes ATP sulphurylase and
luciferase referred to as Enzymatic Luminometric Inorganic
Pyrophosphate Detection Assay ("ELIDA") has been described by Nyren
and Lundin (Anal. Biochem., 151, 504-509, 1985, the entire
disclosure of which is incorporated herein by reference.) The use
of the ELIDA method to detect PPi in a droplet on a droplet
microactuator is one aspect of the present invention. The method
may however be modified, for example by the use of a more
thermostable luciferase (Kaliyama et al., 1994, Biosci. Biotech.
Biochem., 58, 1170-1171, the entire disclosure of which is
incorporated herein by reference). Examples of suitable detection
enzymes for the PPi detection reaction are ATP sulphurylase and
luciferase.
[0172] In certain prior art applications, a nucleotide degrading
enzyme, such as apyrase, is used to degrade unincorporated dNTPs
and excess ATP. When degradation is complete, another dNTP is
added. Since the reaction takes place in a single solution, waste
products continue to build up as sequencing proceeds. An important
aspect of the present invention is that it avoids the requirement
for a nucleotide degrading step. Thus, while in some aspects of the
invention, a nucleotide degrading step may be included, in other
aspects, the systems and methods of the invention specifically omit
a nucleotide degrading step. Thus, for example, the analysis may be
accomplished in the absence of a substantial amount of nucleotide
degrading enzyme, e.g., in the absence of a substantial amount of
apyrase.
[0173] Further, the inventors believe that conducting the
incorporation/conversion/detection reactions in the absence of
substantial build-up of byproducts will produce a more predictable
result. Thus, for example, where single nucleotide stretches are
present in the sample, it is traditionally difficult to distinguish
the specific number of incorporations as the length of the single
nucleotide stretch increases. The inventors believe that the clean
nature of the reaction of the present invention will lead to
greater accuracy and reproducibility for longer single nucleotide
stretches. Thus, for example, the inventors believe that the method
of the invention can accurately detect single nucleotide stretches
having 6, 7, 8, 9 10, 11, 12, 13, 14, 15 or more nucleic acids with
90, 95, 99 or 99.9% accuracy.
8.2.5 Droplet Operation Protocols
[0174] It will be appreciated that, in addition to the protocols
described above, a variety of droplet operation protocols may be
utilized in order to carry out the sequence analyses of the
invention. Thus, for example, conversion to ATP can be accomplished
in a single reaction along with the dNTP incorporation reaction, or
the reactions can be performed stepwise: (1) incorporation of dNTP
to release PPi, followed by (2) conversion of PPi to ATP. Where the
incorporation and conversion steps are performed together, the
system may transport a single droplet including the required
reagents (dNTP, polymerase, ATP sulfurylase, and APS). Thus, all
reagents required to incorporate a dNTP into the immobilized
sample, release PPi, and react the PPi with APS to yield ATP may be
included in a reservoir on the droplet microactuator as a single
source reagent for each nucleotide. The source reagent for each
nucleotide may be successively brought into contact with the
immobilized sample so that the reactions may take place, yielding
ATP in the presence of a complimentary dNTP.
[0175] Where the incorporation and conversion steps are performed
separately, the primer, polymerase, dNTP, sulfurylase, and APS may
be provided from separate sources as separate reagent droplets
which are merged together to perform the reactions of the
invention. Alternatively, some or all of these reagents may be
provided from a single source as a pyrosequencing reagent droplet
which is brought into contact with the immobilized sample in order
to conduct the reactions of the invention. For example, a droplet
including the dNTP and polymerase may be brought into contact with
the immobilized sample, so that the base will incorporate if
complimentary, thereby releasing PPi. The droplet potentially
including the PPi may then be transported away from the immobilized
sample and combined with a droplet including the ATP sulfurylase
and APS to produce ATP. Alternatively, a droplet including the ATP
sulfurylase and APS may be combined with the droplet potentially
including the PPi in the presence of the immobilized sample to
produce ATP.
[0176] Further, while FIG. 4 illustrates the priming step 4 and
incorporation/conversion steps 5 as occurring sequentially, it will
be appreciated that they can be separated out further or they can
all be incorporated into a single step. In other words, each
specific reagent may be added to the reaction at the appropriate
time in one or more droplets or any combination of multiple
reagents may be provided together in a single droplet or series of
droplets. Thus, in one embodiment, the droplet microactuator
transports one or more droplets into contact with the single
stranded sample, wherein one or more droplets together include the
following reagents (or their functional equivalents) provided
together or in separate droplets: primer, polymerase, and dNTP in
any combination and in any order producing the result that the
primer hybridizes with the sample to form a double stranded
portion, the polymerase catalyzes incorporation of any
complimentary dNTP into a target site at the first single stranded
base position adjacent to the double stranded portion, thereby
releasing PPi.
[0177] In another embodiment, the droplet microactuator transports
one or more droplets into contact with the single stranded sample,
and the one or more droplets together include the following
reagents (or their functional equivalents): primer, polymerase,
dNTP, sulfurylase, and APS, in any combination and in any order
producing the result that the primer hybridizes with the sample to
form a double stranded portion, the polymerase catalyzes
incorporation of any complimentary dNTP into a target site at the
first single stranded base position adjacent to the double stranded
portion, thereby releasing PPi, and the ATP sulfurylase converts
any PPi to ATP in the presence of APS. Base incorporation is
determined by quantifying the quantity of PPi released.
[0178] The droplet potentially comprising ATP may be merged via
droplet microactuation techniques with a droplet comprising
reagents, such as luciferase and luciferin, for facilitating
detection of any ATP. Similarly, a droplet including luciferin and
potentially comprising ATP may be merged via droplet microactuation
techniques with a droplet including luciferase for detection of any
ATP. Further, a droplet including luciferase and potentially
comprising ATP may be merged via droplet microactuation techniques
with a droplet including luciferin for detection of any ATP.
[0179] Droplets for the detection reaction may be merged in the
presence of or apart from the immobilized sample. For example, a
luciferase/luciferin droplet may be merged with the droplet
potentially including ATP in the presence of the immobilized
sample. Alternatively, the droplet potentially including ATP may be
separated from the immobilized sample to be merged with a
luciferase/luciferin droplet. In either case, the merging of
droplets including reagents that produce a light signal may be
accomplished in proximity to the sensor in order to maximize the
amount of light detected.
[0180] When the droplet potentially including ATP is transported
away from the immobilized sample to be merged with a luciferase
droplet, the transport step may include an incubation step in order
to maximize the production of ATP for detection in the fluorescence
reaction. In other words, this incubation may be accomplished
during transport, or the droplet may be temporarily stored for
incubation prior to the fluorescence reaction. The droplet
microactuator may include an incubation zone for this purpose. The
incubation zone may or may not include a heating element to control
temperature in the zone. The incubation zone may or may not include
a wall separating the zone from the remainder of the droplet
microactuator. The incubation zone may include an array of
electrodes to facilitate transport of droplets into and out of the
zone. The zone is scalable and may include electrodes for
transporting and storing tens, hundreds or more droplets within the
incubation zone. In the practice of the invention, one or more
detection reagents may be specifically excluded from the polymerase
reaction step so that any signal will not be emitted during the
polymerase reaction. For example, in one embodiment, a detection
enzyme is not added to the reaction mix for the polymerase step.
Instead, the droplet used to conduct the polymerase step is
transported away from the immobilized sample, then merged with a
droplet including the detection enzyme in range of a sensor for
detecting signal from any resulting reaction. The reaction mix for
the polymerase reaction may thus include at least one dNTP,
polymerase, APS, and ATP sulfurylase, and may optionally include
luciferin, while lacking any significant amount of luciferase. In
this way, the dNTP incorporation reaction may be separated from the
detection reaction. The detection reaction may thus be conducted in
the presence of the sensor, e.g., as illustrated in FIG. 5, in
order to maximize the detection signal. For example, where the
detection signal includes light, the detection reaction may be
completed in range of a sensor for detecting light emitted from any
resulting light-producing reaction.
[0181] Further, a detection reaction and a subsequent incorporation
reaction may be conducted in parallel, thereby expediting
sequencing speed. Similarly, an incorporation reaction may be
conducted, the output of a previous incorporation reaction may be
incubated, and the output of a previous incubation may be subjected
to detection all in parallel in separate droplets, thereby
expediting sequencing speed.
[0182] Unlike certain processes of the prior art, the droplet
microactuator approach of the present invention avoids mass
transport effects. Reagents may be brought directly into contact
with each sample, without requiring a flow of reagents across
multiple samples. Where magnetically responsive beads are used,
they may be maintained in place using a magnetic field and/or they
may be transported from place-to-place in droplets. Reagents may be
transported from a reagent source directly to a sample without
coming into contact with other samples and potentially causing
cross-contamination. Diffusion of byproducts is avoided by
isolation of droplets in the filler fluid. Wells packed with beads,
e.g., stabilizing beads, which may interfere with light detection
may also be avoided. A wash containing apyrase may be used between
applications of nucleotides, but its use is not necessary in the
practice of the invention, and in some embodiments, it is
specifically avoided. Between applications of each new set of
reagents to the immobilized sample, it may be washed, e.g., with a
buffer solution. Various surface washing protocols are described in
Section 8.6.
8.2.6 Applications
[0183] The nucleic acid amplification and sequencing methods,
devices and systems of the invention are useful in a wide variety
of settings, such as scientific research, medical and veterinary
diagnostics, phramacogenomics, genomic sequencing, gene expression
profiling, detection of sequence variation, forensics, and
environmental testing. Due to the portable size enabled by the
droplet microactuator of the invention, sequencing for the
applications described herein can, if desirable, be accomplished at
the point-of-sample collection.
[0184] In one embodiment, the invention may provide an influenza
test panel. In this embodiment, the system may accept a biological
sample as input, process the sample to prepare target influenza
virus nucleic acids for amplification, conduct amplification using
the protocols of the invention, and detect the presence of target
influenza nucleic acids. The biological sample may, for example, be
collected from a nasopharyngeal swab.
[0185] In another embodiment, the invention may provide a
respiratory infection panel. In this embodiment, the system may
accept a biological sample as input, process the sample to prepare
nucleic acids from common respiratory pathogens, such as bacteria,
viruses and/or fungi, for amplification, conduct amplification
using the protocols of the invention, and detect the presence of
target respiratory pathogen nucleic acids. In an extended version
of the respiratory infection panel, the panel may include testing
for atypical infections such as those affecting immuno-compromised
patients. The biological sample may, for example, be provided by or
obtained from a nasopharyngeal swab. Examples of respiratory
pathogens suitable for detection using a respiratory infection
panel of the invention include S. pneumoniae, H. influenzae,
Legionella, Chlamydia, Mycoplasma; viruses such as influenza, RSV,
coronavirus, parainfluenzae, adenovirus, metapneumovirus,
bocavirus, hantavirus; and fungi such as Pneumocystis, Aspergillus,
Cryptococcus.
[0186] For sequencing lengthy nucleic acids, e.g., whole genomes,
samples may be broken into smaller overlapping fragments (e.g.,
100-1000 bp, 200-900 bp or 300-800 bp), e.g., by digestion with
restriction enzymes. The smaller fragments may be analyzed using
the systems and methods of the invention. Results may be assembled
and edited to reconstruct the longer sequence, e.g., by identifying
and matching overlaps in the sequenced fragments. Analysis of the
fragments may proceed in a parallel manner, in order to expedite
the sequencing. Each template may be sequenced multiple times to
enhance accuracy. In this way, entire chromosomes or even entire
genomes may be accurately sequenced.
[0187] Genes transcribed in a given set of tissues can be
determined from mRNA extracted from cells or tissue. mRNA may be
copied into DNA (cDNA) using reverse transcriptase. The resulting
cDNAs may be cloned, and the clone ends from a cDNA library may be
sequenced according to the methods of the invention to generate
EST, which provide an expression profile for the tissue from which
the mRNA was extracted. RNA patterns may in some cases be
correlated with disease states and may be sequenced as a diagnostic
tool. RNA viruses may also be sequenced.
[0188] Once a reference sequence has been obtained for a region of
interest (e.g., a gene believed to be involved with a disease),
variations of the sequence as found in different individuals or
closely related species can be identified by selectively
resequencing a small portion of known sequence. Variations may, for
example, occur as SNPs; size differences (insertions/deletions);
copy number differences (duplications) and rearrangements
(inversions, translocations).
[0189] Populations of organisms can be sequenced, e.g., from water,
soil and/or atmospheric samples. For example, most current
knowledge of microbiology still is derived from individual species
that either cause disease or grow readily as monocultures under
laboratory conditions and are thus easy to study. Sequencing can be
used to study the organization, membership, functioning, and
relationship of such organisms. Qualitative analysis of sequence
and gene diversity can thus be obtained from organisms that cannot
be cultured using conventional techniques.
[0190] The systems and methods of the invention may also be used to
provide genomically specific diagnostics and treatment. For
example, the systems may be used to identify genotypic traits that
are associated with more or less favorable treatment outcomes.
Results may be used to guide treatment decisions. Similarly, the
systems and methods of the invention can be used to identify
identifying mutations in infectious organisms or genetically
damaged or altered cells, such as cancers and other neoplasms, and
this information can be used to guide or confirm treatment
decisions. Infectious organisms may, for example, include viruses,
bacteria, parasites or fungi. The invention provides, for example,
a system and method for quick, inexpensive detection of drug
resistant strains of bacterial or viruses (e.g., new strains of
drug-resistant HIV) which is a critical component of combating
these disease causing organisms.
[0191] The systems and methods of the invention may be employed for
genetic testing, e.g., to identify DNA segments in a subject that
play a role in a specific disease or DNA segments which may be
predictive of a specific disease. For example, linkage may be
demonstrated when, within families, one form of the marker is found
in those with the disease more often than in blood relatives in
whom the disease is absent. Such methods have proved successful in
Huntington disease, cystic fibrosis, breast cancer, and other
disorders. Thus, for example, the systems and methods of the
invention may be used to identify mutations in a gene that are only
present (in gene dosage sufficient to cause disease) in subjects
with disease or subjects predisposed to develop the disease. In
another embodiment, the systems and methods of the invention are
used to identify genetic variations for which (1) there is a
statistically significant probability that the sequence will be
present in people with the disease, and (2) there is a
statistically significant probability that the sequence will not be
present in people without the disease. Similarly, the systems and
methods of the invention are used to identify genetic variations
for which there is a statistically significant probability that
people with positive test results will get the disease and that
people with negative results will not get the disease. Further, the
systems and methods of the invention may be used to sequence a
segment of DNA to identify one or more SNPs.
[0192] The systems and methods of the invention may be used in a
clinical trial setting. For example, nucleic acids from persons
participating in a trial may be sequenced, and adverse events may
be compared with genetic variation in the trial group to identify a
subset of participants with increased susceptibility to one or more
adverse events. Depending on the severity of the particular adverse
event in question, subjects with the associated genetic variation
may, for example, be watched more closely, receive further
protective treatment, and/or removed from the trial altogether.
Similarly, efficacy may be compared with genetic variation in the
trial group to identify a subset of participants with increased
likelihood to positive treatment outcomes. Target populations can
be defined based on positive outcomes and/or lack of unduly adverse
events. Products can be labeled accordingly. Physicians can test
their patients for the associated genetic variation and can
prescribe products only to the population subset for which
treatment is pharmaceutically acceptable.
[0193] The invention is also useful for forensic evaluations, such
as: identifying potential suspects whose DNA may match evidence
left at crime scenes; exonerating persons wrongly accused of
crimes; identifying crime and catastrophe victims; establishing
paternity and other family relationships; identifying endangered
and protected species as an aid to wildlife officials; detecting
bacteria and other organisms that may pollute air, water, soil, and
food; matching organ donors with recipients in transplant programs;
determining pedigree for seed or livestock breeds; and
authenticating consumables such as caviar and wine; identifying
genetically modified foods.
[0194] Other examples of applications include: testing for
associations between genetic variations and subject outcomes, e.g.,
efficacy, side effect profile, pharmacokinetics, and/or
pharmacodynamics, in the drug discovery process; analyzing a
subject's genetic profile to differentiate between potential drug
therapies based on genotypic variation; screening for
predisposition for disease so that a subject can take steps to
monitor, treat, avoid or lessen the severity of a genetic disease;
screening to decrease the number of adverse drug reactions in a
patient population; screening to enable the use of a drug which is
not safe in a genetically identifiable population subset; and
monitoring of gene therapies.
8.3 Affinity-Based Assays
[0195] The invention provides methods, devices and systems for
conducting droplet-based, affinity-based assays, such as
affinity-based assays. These assays include any assay in which a
compound having a binding affinity for an analyte is contacted with
the analyte or a sample potentially including the analyte using
droplet operations. For example, the compound having a binding
affinity for an analyte may be provided in a droplet and
transported into contact with an analyte which is present in
another droplet on a droplet microactuator or is immobilized on a
surface of a droplet microactuator. As another example, the
compound having binding affinity for the analyte may itself be
immobilized on the surface of a droplet microactuator and/or on the
surface of beads included on a droplet microactuator, and a droplet
including the analyte or potentially including the analyte may be
brought into contact with the immobilized antibody.
[0196] It will be appreciated that a wide variety of affinity-based
assay protocols are possible within the scope of the invention.
Examples of affinity-based assay formats include direct
affinity-based assays, indirect affinity-based assays, and
competitive affinity-based assays. The assays may be employed to
detect the presence of a target analyte, and may also in some cases
be used to quantify the target analyte present in a sample. In a
competitive assay, a droplet including a sample antibody and
labeled antibody is contacted with a surface. The sample antibody
competes with labeled antibody for binding to antigen adsorbed onto
the surface. A variant of this approach involves linking the
antigen to the surface via an intermediary linker. For example, the
linker may be an antibody. The capture bridge assay uses a droplet
including a sample antibody to link antigen adsorbed to the surface
with antigen in solution. Another approach involves the use of
biotinylated antigen and a streptavidin coated solid phase. Another
approach involves binding the sample antibody to antigen
immobilized on the solid phase. The bound antibody may be detected
with isotype specific labeled second antibody. Excess antibody can
be washed off using the droplet protocols of the invention.
[0197] It will be appreciated that an important aspect of the
invention involves the ability to conduct droplet operations using
each of the required affinity-based assay reagents and/or samples
on a droplet microactuator. For example, the invention includes:
[0198] (1) a droplet microactuator comprising thereon a droplet
comprising any one or more of the reagents and/or samples described
herein for conducting affinity-based assays; [0199] (2) a device or
system of the invention comprising such droplet microactuator;
[0200] (3) a method of conducting droplet operations on or
otherwise manipulating a droplet making use of such droplet
microactuator or system; and/or [0201] (4) a method of conducting
an droplet-based affinity-based assay making use of such droplet
microactuator or system.
[0202] For example, the droplet operations may include one or more
of the following: loading a droplet into the droplet microactuator;
dispensing one or more droplets from a source droplet; splitting,
separating or dividing a droplet into two or more droplets;
transporting a droplet from one location to another in any
direction; merging or combining two or more droplets into a single
droplet; diluting a droplet; mixing a droplet; agitating a droplet;
deforming a droplet; retaining a droplet in position; incubating a
droplet; heating a droplet; vaporizing a droplet; cooling a
droplet; disposing of a droplet; transporting a droplet out of a
droplet microactuator; other droplet operations described herein;
and/or any combination of the foregoing. Various other methods,
devices, systems, and other aspects of the invention will be
apparent from the ensuing discussion.
8.3.1 Samples and Sample Preparation
[0203] The invention provides droplet-based affinity-based assays
which are useful for detection of a wide variety of analytes. For
example, any analyte that can bind with specificity to an affinity
molecule, such as an antibody, is suitable for detection using the
systems of the invention. A single sample may be analyzed for one
or more target analytes. Analytes may, for example, be biological
analytes or synthetic analytes. Examples include analytes in the
following categories: analytes from human sources, analytes from
animal sources, analytes from plant sources, analytes from
bacterial sources, analytes from viral sources, and analytes from
spore sources. Analytes may, for example, include proteins,
peptides, small molecules, and various biomolecules, such as
carbohydrates, lipids, and the like. In one embodiment, samples are
contacted with immobilized antibody (e.g., antibody immobilized on
beads), prior to introduction of the immobilized antibody onto the
droplet microactuator.
[0204] An illustrative droplet microactuator 600 suitable for
conducting immunoassays is illustrated in FIG. 6. This embodiment
may employ two substrates, a first substrate 601a and a second
substrate 601b spaced apart in a substantially parallel fashion to
provide an intervening space. Multiple fluid ports or reservoirs
may be provided in the intervening space, such as wash buffer
reservoirs 602, sample reservoir 604, primary antibody reservoir
606, secondary antibody reservoir 608, and immobilized antibody
(e.g., antibody immobilized on beads) reservoir 610. Waste areas
612 may also be provided, as well as a magnet 614 positioned in a
manner which permits interaction between the magnet's magnetic
field and magnetically responsive components located in the
intervening space. In this particular embodiment, transport
electrodes 616 are provided on the first substrate.
8.3.2 Sandwich Affinity-Based Assay
[0205] In one embodiment, the invention provides a droplet-based
sandwich affinity-based assay performed on a droplet microactuator.
It will be appreciated that a wide variety of protocols are
possible within the scope of the invention for conducting sandwich
affinity-based assays.
[0206] The following droplet-based protocol, which is based on the
FIG. 7 illustration, is provided as one example only and is not
intended to be limiting of the scope of the invention: [0207] (1)
immobilizing on a surface an antibody (primary) with specificity
for a target analyte; [0208] (2) washing the immobilized antibody,
e.g., using a droplet-based washing protocol, to remove excess
antibody; [0209] (3) using droplet operations to expose the
immobilized antibody to a sample droplet potentially including the
target analyte with binding affinity for the immobilized antibody;
[0210] (4) washing the immobilized antibody-target analyte complex,
e.g., using a droplet-based washing protocol, to remove unbound
components of the sample droplet; [0211] (5) exposing the
immobilized antibody (now potentially including the target analyte
bound thereto) to a droplet including a reporter (secondary)
antibody; [0212] (6) washing away excess reporter antibody, e.g.,
using a droplet-based washing protocol; [0213] (7) optionally,
performing additional steps to provide a measurable parameter or
signal; [0214] (8) measuring the measurable parameter or signal;
and [0215] (9) providing an output indicative of the signal.
[0216] Any one or more of the foregoing steps can be performed
using droplet operations on a droplet microactuator as described
herein.
8.3.2.1 Immobilizing Antibody
[0217] A primary antibody is immobilized on a surface. The surface
may, for example, be a surface of the droplet microactuator, or the
surface of beads, such as magnetically responsive beads,
non-magnetically responsive beads, or particles, such as
nanoparticles.
[0218] Immobilization of the antibody to the surface can be
accomplished on the droplet microactuator using droplet-based
protocols. For example, reagents for immobilizing an antibody to a
surface may be introduced to the droplet microactuator, dispensed
as discrete droplets and transported into contact with the surface
for deposition. Where the surface in question is the surface of one
or more beads, the beads may be introduced to the droplet
microactuator, dispensed as buffer droplets, transported on the
droplet microactuator, and merged with one or more droplets
including reagents for immobilizing the droplets on the surface of
the beads.
[0219] Alternatively, the antibodies may be immobilized off the
droplet microactuator. For example, antibodies may be immobilized
on beads prior to introduction to the droplet microactuator. A
variety of protein-coated (e.g., streptavidin) and antibody-coated
beads are commercially available. In another embodiment, antibodies
may be immobilized on a surface of the droplet microactuator, e.g.,
during manufacture of the droplet microactuator.
[0220] Further, surfaces may be prepared for immobilization of
antibodies. For example, a surface may be provided including
moieties which have an affinity for an antibody or a binding moiety
coupled to an antibody. The antibody, optionally including the
binding moiety, may be brought into contact with the surface
thereby immobilizing the antibody on the surface. For example,
beads pre-coated with streptavadin may be introduced to the droplet
microactuator. Droplet operations may be conducted with droplets
including the streptavadin-coated beads, and may be employed to
bring such bead-containing droplets into contact with one or more
droplets including biotinylated antibody to thereby couple the
antibody to the beads. As another example, the droplet
microactuator may include a streptavidin coated surface on a
droplet microactuation path, such that droplet operations may be
employed to bring a droplet including biotinylated antibody into
contact with the streptavidin coated surface and thereby immobilize
the antibody on the surface. In a yet another example, capture
antibodies can be selectively immobilized onto the surface of the
droplet microactuator, e.g., by patterning the surface to enable
immobilization of antibodies or by coupling photoactive species
directly to the antibodies or to streptavidin and then immobilizing
the antibody selectively by using a direct-write light system or
using an optical mask or using other means to selectively expose
light.
[0221] A wide variety of techniques are available for binding
antibodies to surfaces. For example, the surface may be activated
with Protein G to enable the binding of antibody molecules via
their Fc domain, leaving the variable region available for target
capture. Antibody may be covalently bound to latex surfaces by
reaction of activated antibody with 1,3-diaminopropane coupled,
polystyrene aldehyde/sulfate latex. Surfactant-free sulfate white
polystyrene latex beads may be coated with antibody by incubation
with antibody and conjugation buffer (30 mM Na.sub.2CO.sub.3, 70 mM
NaHCO.sub.3, pH 9.5). Biotinylated antibody can be captured on
streptavidin coated substrates. Antibodies may be covalently bound
to a modified surface of the droplet microactuator such as a silane
or thiolated layer. Antibodies may be covalently bound to a
modified surface of the droplet microactuator (e.g., during
assembly or using droplet operations to deposit the antibodies on
the surface), such as a surface modified with silane or a thiolated
surface.
8.3.2.2 Binding Target Analyte to Immobilized Antibody
[0222] A sample droplet is contacted with the immobilized antibody
to permit any target analyte present in the sample to bind with the
immobilized antibody. This step may be accomplished using droplet
operations to transport a sample droplet into contact with the
surface on which the antibody is attached, e.g., a droplet
including antibody coated beads or a surface of the droplet
microactuator on which the antibody is immobilized. In an
alternative embodiment, the surface is a beads surface, and the
bead is contacted with the sample prior to introduction into the
droplet microactuator. The bead may also be washed prior to
introduction into the droplet microactuator. The antibody binds to
analyte from the sample droplet. The binding process may be
expedited by increasing the speed of mass-transport. A few examples
of accelerating mass transport include transport of the droplets at
a high speed to enable thorough mixing of the beads with antibodies
and the target analyte or to replenish the surface of immobilized
antibody with target analytes. Other means include agitating the
incubated droplet in-place by electrically manipulating the droplet
or by a number of external means such as piezoelectric methods of
actuation. In absence of any means of mass transport, the binding
events occur based on diffusion and it could take longer times
thereby prolonging the assay times. The immobilized antibody (e.g.,
the beads or the surface) may in some embodiments be subjected to a
washing protocol on the droplet microactuator, e.g., as described
in Section 8.6, to remove excess sample or other materials.
8.3.2.3 Binding Reporter Antibody to Target Analyte
[0223] After washing (e.g., the beads or the surface), a droplet
comprising a reporter antibody having affinity for a different
epitope on the analyte may be brought into contact with the washed
immobilized antibody potentially having the captured analyte. The
labeled antibody conjugate includes an antibody coupled to a
reporter molecule, such as a radioactive molecule, an enzyme
capable of catalyzing a detectable reaction (e.g., a color change,
chemiluminescence, fluorescence, chemiluminescence, or
electrochemical), a chemiluminescent molecule, or a fluorescent
molecule. Depending on the reporter used, the immobilized antibody
(e.g., beads or other surface) including the analyte and reporter
antibody may then subjected to a washing protocol, e.g., as
described in Section 8.6, to remove excess reporter antibody.
8.3.2.4 Producing and Detecting Measurable Parameter
[0224] Bound reporter antibody may be quantified by detecting a
signal facilitated by the reporter antibody. For example, the
signal may be radioactivity, color change, luminescence,
fluorescence, luminescence, Raman spectra, light scattering
approaches, particle/bead aggregation, surface plasmon resonance,
Raman spectroscopic effect and the like. The detection may be
direct or indirect, by detecting the quantity of antibody coupled
to the analyte or by detecting the quantity of unbound
antibody.
[0225] For approaches requiring further reaction to produce a
signal, e.g., conversion of a non-fluorescent product to a
fluorescent product, a droplet including the additional required
reactants can be brought into contact with
antibody-antigen-antibody complex in order to facilitate the
further reaction.
[0226] Once the reporter antibody has been permitted to bind to the
analyte, excess reporter antibody can be washed away using a
washing protocol, and droplet operations can be used to bring a
droplet including the required reporter reactants into contact with
the immobilized antibody. In one embodiment, the reporter antibody
is labeled with an enzyme (e.g., horseradish peroxidase (HRP) or
alkaline phosphatase (ALP)) capable of catalyzing a reaction which
produces a measurable parameter. For example, HRP can be used to
catalyze hydrogen peroxide to generate an electrochemical signal
which can be detected by measuring the current or voltage.
Detection of bound antibody can be achieved by a fluorescence
reaction catalyzed by the HRP using Amplex Red and hydrogen
peroxide as substrates. Another example employs an alkaline
phosphatase mediated conversion of NBT to violet formazan, which
can be detected in a droplet colorimetrically. In another approach,
a chemiluminescence substrate such as luminol or Ps-atto from
Lumigen could be catalyzed by HRP to generate a chemiluminescence
signal. Other examples of suitable detection approaches are
discussed elsewhere herein (e.g., see 8.3.5).
[0227] In one embodiment, the detection step is performed in a
droplet on the droplet microactuator in the presence of a sensor in
order to enhance or maxinize capture of signal from the reaction.
In another embodiment, the reaction is performed away from a
sensor, and the droplet is transported using droplet operations
into the presence of a sensor for detection purposes.
8.3.2.5 Alternative Sandwich Assay Approaches
[0228] It will be appreciated that a variety of alternative
approaches are possible. For example the steps need not be
performed in the order described above, e.g., the reporter antibody
may be bound to the analyte prior to or at the same time the
analyte is exposed to the immobilized antibody. In another
approach, binding of capture antibody, analyte, and reporter
antibody can all be performed simultaneously and then presented to
a capture site and then washed. In some approaches, such as surface
enhanced resonance Raman scattering, washing may not be
required.
8.3.3 Competitive Affinity-Based Assay
[0229] In one embodiment, the invention provides a competitive
affinity-based assay performed on a droplet microactuator. Analytes
for detection by competitive affinity-based assay are typically
those that are too small for binding two antibodies as required by
a sandwich assay. It will be appreciated that a wide variety of
protocols are possible within the scope of the invention for
conducting competitive affinity-based assays. The following
droplet-based protocol, which is based on the FIG. 8 illustration,
is provided for illustration only and is not intended to be
limiting of the scope of the invention: [0230] (1) immobilizing on
a surface an antibody with specificity for a target analyte; [0231]
(2) washing the immobilized antibody, e.g., using a droplet-based
washing protocol, to remove excess antibody; [0232] (3) providing a
sample droplet potentially including target analyte and including a
reporter analyte; [0233] (4) exposing the immobilized antibody to
the combined target analyte/reporter analyte droplet so that the
reporter analyte competes with any target analyte for binding
sites; [0234] (5) washing the substrate to remove unbound analyte
and reporter analyte; [0235] (6) optionally, performing additional
steps to yield a measurable parameter or signal; and [0236] (7)
quantifying bound reporter analyte, wherein the quantity of
reporter analyte is inversely proportional to the quantity of
target analyte.
[0237] Any one or more of the foregoing steps can be performed
using droplet manipulation techniques on a droplet microactuator as
described herein. Each of the steps is discussed in further detail
in the ensuing sections.
8.3.3.1 Immobilizing Antibody
[0238] The antibody may be immobilized as described above in
Section 8.4.1.1.
8.3.3.2 Competitive Binding
[0239] A droplet including the sample potentially including a
target analyte is combined with a droplet including the reporter
analyte, and the combined droplet is brought into contact with the
immobilized antibody. Alternatively, the mixture of target and
reporter is accomplished during loading of the droplet
microactuator.
[0240] The reporter analyte may be made by coupling the reporter
nucleic acid to the analyte using any of a variety of conjugation
methods. In one embodiment, the analyte portion is modified with a
molecule, such as biotin, which generates a secondary capture site
for immobilizing a streptavidin sensor DNA complex. The coupling of
biotin to the analyte must not unduly interfere with its binding to
the capture antibody. The biotinylated material may in some cases
compete equally with the analyte from the test sample. Coupling of
the biotinylated analyte to a reporter molecule can occur before or
after the biotinylated analyte is captured by the immobilized
antibody.
[0241] For example, in one embodiment, the assay is performed by
mixing a droplet with a known quantity of biotinylated analyte with
the sample droplet potentially containing an unknown quantity of
unmodified analyte. A droplet including the biotinylated analyte is
combined with a droplet potentially including the target analyte.
The combined droplet is contacted with the immobilized antibody so
that the biotinylated analyte and the target analyte (if any)
compete for binding to the immobilized antibody. The quantity of
biotinylated analyte bound is inversely proportional to the
quantity of analyte in the test droplet. The immobilized antibody
(e.g., the beads or the surface) may then be subjected to a washing
protocol, e.g., as described in Section 8.6, to remove excess
reporter analyte.
8.3.3.3 Detecting the Reporter Analyte
[0242] After washing, a droplet with a streptavidin-biotin-reporter
complex is added to a droplet including the washed beads or
otherwise brought into contact with a surface including the
immobilized antibody. The streptavidin-biotin-reporter complex
binds to any biotinylated analyte that was captured by the antibody
on the bead.
8.3.3.4 Alternative Competitive Assay Approaches
[0243] The competitive affinity-based assay described here is only
one example of a droplet microactuator protocol suitable for
execution on the droplet microactuator of the invention. A variety
of alternatives are possible within the scope of the invention. For
example, the steps are not limited to the order given. The antibody
can be bound to the target analyte/reporter analyte before it is
immobilized by combining a droplet including the free antibody with
one or more droplets including the target analyte/reporter analyte,
after which the antibody may be brought into contact with the
surface for immobilization. The reporter analyte may be conjugated
with the reporter nucleic acid on the droplet microactuator by
combining droplets including the two reagents. A droplet including
the reporter analyte may be combined with a droplet including the
reporter nucleic acid to affect conjugation before or after the
reporter analyte is exposed to the captured antibody.
[0244] In another embodiment, a competitive assay is performed by
mixing a droplet with a known amount of enzyme-labeled analyte with
a sample droplet containing the target analyte which is then
further mixed with a droplet containing antibodies. Competition
ensues for binding sites between the labeled and target analytes.
The activity of the enzyme is reduced upon binding of the
enzyme-labeled analyte with the antibody and this can be monitored
through a number of different types of transduction events, e.g.,
absorbance, in order quantify the concentration of the target
analyte in the sample. For example, a droplet containing Vancomycin
labeled with glucose-6-phophate dehydrogenase (G6P-DH) can be mixed
with a sample droplet containing unlabelled Vancomycin which can be
further mixed with a droplet containing antibodies reactive to
Vancomycin, glucose-6-phosphate, and nicotinamide adenine
dinucleotide (NAD). The activity of G6P-DH is reduced upon binding
to an antibody. G6P-DH converts NAD.sup.+ to NADH, resulting in an
absorbance change that is measured spectrophotometrically at 340
nm. Once a calibration has been performed within the droplet
microactuator, the Vancomycin concentration in each unknown sample
can be determined using the stored calibration curve and the
measured absorbance obtained in the assay of the sample. Other
analytes that can be detected using the same method includes
Valproic acid, Tobramycin, Gentamicin, and Caffeine.
8.3.4 Other Affinity-Based Assay Protocols
[0245] The competitive affinity-based assay described here is only
one example of a droplet microactuator protocol suitable for
execution on the droplet microactuator of the invention. A variety
of alternatives are possible within the scope of the invention. For
example, the droplet microactuator system of the invention enables
multiple affinity-based assays to be simultaneously performed on a
single sample or a single affinity-based assay to be performed on
multiple samples or a combination thereof. Further, affinity-based
assays may be performed along with other tests, such as PCR and/or
immuno-PCR.
[0246] A variety of alternative assay types may be executed using
droplet-based protocols in light of the instant specification.
Examples include immunoprecipitation assays; immunoradiometric
assays; heterogeneous enzyme labeled affinity-based assays in which
the quantitation of the antibody bound and unbound fractions
requires a physical separation of these two fractions; homogeneous
(non-separation) enzyme labeled affinity-based assays which do not
require a physical separation of these two fractions because the
unbound and antibody bound fractions can be distinguished
functionally. For immunoprecipitation assays, droplets including
reagents for conducting the immunoprecipitation assays are combined
on a droplet microactuator to conduct the immunoprecipitation
assay. Immunoprecipitation may be detected using a light scattering
detector.
[0247] While most of the approaches discussed thus far involve
immobilization of the antibody or the analyte, immobilization is
not required in all droplet-based immunoassays of the invention.
For example, the invention includes a homogenous droplet-based
enzyme-multiplied immunoassay in which the labeled antibody
includes an enzyme that is inactivated when bound to the primary
antibody. Enzymatic activity is approximately proportionate to the
analyte concentration. The approach generally includes combining on
a droplet microactuator droplets for conducting the droplet-based
enzyme-multiplied immunoassay and measuring the resulting enzymatic
activity.
[0248] In another method, the light scattering properties of the
antigen/antibody complex will be altered upon a binding event, and
this change can be monitored by detecting light scattering changes
in the reaction droplet on the droplet microactuator, such as
turbidity measurements, to identify and/or quantitate the capture
events. For example, a physiological sample droplet on the droplet
microactuator containing immunoglobulins such as IgA, IgG, and IgM
(after sample preparation including dilution and addition of
polymers) or apolipoproteins such as ApoA1, ApoB (after sample
preparation including dilution and addition of polymers or
surfactants) can be combined using droplet operations with a
droplet containing respective antibodies that, upon occurrence of
binding events, results in a change in the turbidity of the
combined droplet which can be monitored spectrophotometrically. A
few examples of other analytes that can be measured using this
technique include .alpha..sub.1-antitrypsin (AAT), transferrin,
prealbumin, haptoglobin, complement C3, and complement C4.
[0249] Another class of immunoassays suitable for use in the
present invention include agglutination assays which can also be
performed in the droplet format. A droplet containing the analyte
is mixed with a droplet containing particles, for example latex
particles, with the capture antibody or antigen bound to the
particles. If the target analyte is present in the sample, the
latex particles start to agglutinate together and it can be
quantified by measuring the absorbance.
[0250] The system provides multiplexed affinity-based assays. In
one embodiment, the system has the ability to detect 2, 3, 4, 5, 6,
7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or more analytes using
immunoassays. In some high throughput settings, the system provides
for multiplexed detection of 96, 384, 1536, or higher number of
analyses either in serial fashion on in parallel fashion. The
analytes may, for example, include analytes from natural or
non-natural sources. In another embodiment, the invention has the
ability to execute affinity-based assay protocols for detecting one
or more analytes from any 2, 3, 4 or 5 the following categories:
analytes from bacterial sources, analytes from viral sources,
analytes from fungal sources, protein toxin analytes, and small
molecule toxin analytes.
[0251] The system may be programmed to repeat assays as needed to
increase confidence for a single target result. Importantly, the
droplet microactuator system can be programmed to effect
confirmatory re-testing of positives to reduce the possibility of
false positives. The system may also be programmed and configured
to permit storage of tested samples on the droplet microactuator
for subsequent additional laboratory testing.
[0252] An important advantage of the invention is the capability of
the droplet microactuator to quickly and accurately produce
calibration curves. The droplet microactuator can accurately and
reproducibly dispense droplets of a solution of known concentration
of control analyte and can dilute such droplets by combining them
with buffer droplets to provide a series of control droplets having
varied concentrations of control analyte. These control droplets
can be taken through the same protocol as sample droplets to
produce a calibration curve. The calibration curve can be used to
determine quantities of analyte in sample droplets.
8.3.5 Other Detection Approaches for Affinity-Based Assays
[0253] A wide variety of detecting approaches are available for use
in the droplet-based affinity-based assays of the invention. The
selected approach will be capable of directly or indirectly
producing a signal in a droplet-based affinity-based assay. The
signal may be detectable by a sensor positioned in contact with or
in close proximity with the droplet. Examples of signals suitable
for use in the affinity-based assays include signals produced from
radioisotopic labels, fluorescent labels, luminescent labels,
electroluminescent labels microparticles, nanoparticles, enzymatic
reactions, aggregation compounds, Raman-active dyes, electroactive
labels, and labels affecting conductivity. Examples of suitable
radioisotopic labels include .sup.57Co, .sup.3H, .sup.35P,
.sup.35S, and .sup.125I. In one embodiment, radioisotopic labels
are used in a scintillation proximity assay (SPA) on a droplet
microactuator. SPA's enable detection of binding events without
requiring a washing step. The radiolabel may, for example, be
incorporated into a competitive analyte in a competition assay or
in a secondary antibody in a sandwich assay. Radiolabels that emit
alpha or weak beta particles are preferred. The SPA is conducted in
proximity to a fluorophore that emits light upon exposure to a
radiolabel. For example, the fluorophore may be provided in a bead,
in a surface of the droplet microactuator to which an antigen or
primary antibody is bound, or in nanoparticle coupled to an antigen
or primary antibody. Examples of suitable luminescent labels
include acridinium ester, rhodamine, dioxetanes, acridiniums,
phenanthridiniums and various isoluminol derivatives. Examples of
suitable fluorescent labels include fluorescein and Eu.sup.3+.
Examples of suitable enzymatic labels include those which produce
visible, colored, fluorescent and/or luminescent products from
suitable substrates. For example, suitable enzymes may include
penicillinase, horseradish peroxidase, .beta.-galactosidase,
urease, deaminases and alkaline phosphatase. Examples of suitable
nanoparticles include metal nanoparticles. Further information
about detection approaches suitable for affinity-based assays of
the invention is provided in Section 8.11.
8.3.6 Sample Size and Assay Speed
[0254] Implementation on a digital microfluidic platform will
dramatically reduce the equipment size and cost, primarily by
miniaturizing all liquid handling functions. Assays can, in some
embodiments, be performed on less than 100.sup.th or 1000.sup.th of
the sample and reagent volumes currently used with equal
sensitivity and specificity. In one embodiment, the system will
typically perform affinity-based assays using samples at droplet
volumes of 1 .mu.L or less, or 100 nanoliters or less.
[0255] Other advantages include reduced time to results due to
faster kinetics in the miniaturized format for the assays and
higher throughput due to multiplexing. For example, in one
embodiment, the system executes affinity-based assay protocols for
detecting 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,
35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or
more analytes in less than about 60, 50, 40, 30, 20, 15, 10, 5 or 2
minutes.
8.3.7 Applications of Droplet-Based, Affinity-Based Assays
[0256] As noted above, the affinity-based assays of the invention
are useful for detecting a wide variety of molecules. Any molecule
which binds with affinity to an affinity molecule, such as an
antibody, is a suitable analyte. Analytes may, for example, include
biological molecules or synthetic molecules. Biological molecules
may, for example, include molecules from plants, animals, microbes,
and viruses. Synthetic molecules may, for example, include
industrial byproducts, pollutants, and pharmaceuticals. Analytes
may include toxins or analytes indicative of the presence of
specific biological organisms, e.g., infectious diseases, or toxins
that are employed in bioterrorism or biological warfare. Examples
of such organisms include anthrax, avian influenza, botulism,
hantavirus, legionnaires' disease, pneumonic plague, smallpox,
tularemia, and viral hemorrhagic fevers (VHFs). Other examples
include analytes associated with monitoring the immunogenicity of
vaccines targeting cancer, chronic infectious diseases (e.g., HIV,
malaria, hepatitis C, candidemia), immunology (e.g., allergy,
autoimmunity), endocrinology (thyroid, non-thyroid), drug testing
(e.g., drugs of abuse, therapeutic drugs) and detection of
bioterrorism agents (e.g., anthrax, smallpox).
[0257] In one embodiment, immunoassay technique is used to test a
sample for the presence of a biological organism, such as a
bacteria or a virus. In some embodiments, the system can achieve
extremely sensitive detections even down to a single cell. Further,
some embodiments may include PCR bacterial typing or variance.
[0258] The affinity-based assays of the invention are also useful
for detecting chemical, biological or explosive threats. For
example, antibody to explosives can be used to detect the presence
of trace amounts of explosive in a sample. Thus, the invention also
provides a method of screening an area for chemical or biological
analytes indicative of the presence of biological, chemical, or
explosive weapons.
[0259] In one embodiment, the invention provides the capability of
detecting multiple analytes in a single droplet. One way to achieve
this result according to the invention involves the use of
different antibodies for different analytes at spatially separated
locations on the droplet microactuator. For example, the droplet
microactuator may include multiple surfaces, each comprising a
specific antibody. A single sample droplet may be manipulated to
come into contact with these antibodies all at once, or
sequentially, as the droplet is transported across the antibody
regions. Affinity-based assay protocols of the invention may be
employed to detect the presence of analyte bound to the antibody in
any of the various regions. Similarly, multiple analytes can be
detected in a single droplet by using different labels to
simultaneously detect different analytes in the same spatial area.
In another embodiment, the droplet microactuator includes spatially
separated beads, each bead or set of beads having a unique antibody
or set of antibodies. Sample droplets and/or bead containing
droplets may be manipulated using droplet operations in order to
contact a sample droplet with each of the beads or sets of
beads.
8.4 Immuno PCR
[0260] The invention provides a droplet-based immuno PCR (pick) for
sensitively detecting analytes that are available only at trace
levels. This invention combines the various means of affinity-based
assays using a detector antibody on a droplet-based platform and
utilizes a nucleic acid strand as a label. This nucleic acid strand
is amplified using amplification techniques (e.g., see Section
8.1).
[0261] It will be appreciated that an important aspect of the
invention involves the ability to conduct droplet operations using
each of the required iPCR reagents and/or samples on a droplet
microactuator. For example, the invention includes: [0262] (1) a
droplet microactuator comprising thereon a droplet comprising any
one or more of the reagents and/or samples described herein for
conducting iPCR protocols; [0263] (2) a device or system of the
invention comprising such droplet microactuator; [0264] (3) a
method of conducting droplet operations on or otherwise
manipulating a droplet making use of such droplet microactuator or
system; and/or [0265] (4) a method of conducting an droplet-based
affinity-based assay making use of such droplet microactuator or
system.
[0266] For example, the droplet operations may include one or more
of the following: loading a droplet into the droplet microactuator;
dispensing one or more droplets from a source droplet; splitting,
separating or dividing a droplet into two or more droplets;
transporting a droplet from one location to another in any
direction; merging or combining two or more droplets into a single
droplet; diluting a droplet; mixing a droplet; agitating a droplet;
deforming a droplet; retaining a droplet in position; incubating a
droplet; heating a droplet; vaporizing a droplet; cooling a
droplet; disposing of a droplet; transporting a droplet out of a
droplet microactuator; other droplet operations described herein;
and/or any combination of the foregoing. Various other methods,
devices, systems, and other aspects of the invention will be
apparent from the ensuing discussion.
8.4.1 Sandwich iPCR
[0267] In one embodiment, the invention provides a droplet-based
sandwich iPCR performed on a droplet microactuator. In general, the
sandwich iPCR involves: [0268] (1) immobilizing on a surface an
antibody with specificity for a target analyte; [0269] (2) washing
the immobilized antibody, e.g., using a droplet-based washing
protocol; [0270] (3) exposing the immobilized antibody to a sample
droplet potentially including the target analyte; [0271] (4)
washing the immobilized antibody, e.g., using a droplet-based
washing protocol; [0272] (5) exposing the immobilized antibody (now
potentially including the target analyte bound thereto) to a
droplet including a second antibody conjugated to a nucleic acid
molecule; [0273] (6) washing the immobilized antibody, e.g., using
a droplet-based washing protocol; [0274] (7) amplifying the nucleic
acid and detecting the amplification (if any) to determine the
presence and quantity of captured target analyte.
[0275] Any one or more of the foregoing steps can be performed
using droplet manipulation techniques on a droplet microactuator as
described herein. Each of the steps is discussed in further detail
in the ensuing sections.
8.4.1.1 Immobilizing Antibody
[0276] A primary antibody is immobilized on a surface. The surface
may, for example be a surface of the droplet microactuator, or the
surface of beads, such as magnetically responsive beads.
Immobilization of the antibody to the surface can be accomplished
on the droplet microactuator using droplet-based protocols. For
example, reagents for immobilizing an antibody to a surface may be
introduced to the droplet microactuator, dispensed as discrete
droplets and transported into contact with the surface for
deposition. Where the surface in question is the surface of one or
more beads, the beads may be introduced to the droplet
microactuator, dispensed as droplets in a buffer, transported, and
merged with one or more droplets including reagents for
immobilizing the droplets on the surface of the beads.
[0277] A wide variety of techniques are available for binding
antibody to surfaces. For example, the surface may be activated
with Protein G to enable the binding of antibody molecules via
their Fc domain, leaving the variable region available for target
capture. Antibody may be covalently bound to latex surfaces by
reaction of activated antibody with 1,3-diaminopropane coupled,
polystyrene aldehyde/sulfate latex. Surfactant-free sulfate white
polystyrene latex beads may be coated with antibody by incubation
with antibody and conjugation buffer (30 mM Na.sub.2CO.sub.3, 70 mM
NaHCO.sub.3, pH 9.5). Biotinylated antibody can be captured on
streptavidin coated substrates. Light-directed immobilization can
also be performed, e.g., as described elsewhere in the present
disclosure.
8.4.1.2 Binding Target Analyte to Immobilized Antibody
[0278] A sample droplet is contacted with the immobilized antibody
to permit any target analyte present in the sample to bind with the
immobilized antibody. This step may be accomplished by transporting
a sample droplet into contact with a surface of the droplet
microactuator on which the antibody is immobilized. In another
embodiment, the step may be accomplished by merging a sample
droplet with a droplet including beads on which the antibody has
been immobilized. The antibody binds to the analyte from the sample
droplet. The immobilized antibody (e.g., the beads or the surface)
may be subjected to a washing protocol, e.g., as described in
Section 8.6.
8.4.1.3 Binding Antibody-NA to Target Analyte
[0279] After washing (e.g., the beads or the surface), a droplet
comprising an antibody-NA conjugate having affinity for a different
epitope on the analyte may be brought into contact with the washed
immobilized antibody potentially having the captured analyte. The
antibody-NA conjugate includes a nucleic acid molecule coupled to
the antibody. The nucleic acid molecule serves as the nucleic acid
template for amplification. The immobilized antibody (e.g., the
beads or the surface) are then subjected to a washing protocol,
e.g., as described in Section 8.6.
8.4.1.4 Amplifying the Nucleic Acid
[0280] The nucleic acid is amplified, e.g, as described in Section
8.1. The quantity of amplified product produced is measured, e.g.,
using real time fluorescence detection, electrochemical and/or
electrochemiluminescent detection. The quantity of PCR product
produced correlates with the quantity of bound antibody-DNA, which
depends in turn on the quantity of analyte present in the sample
droplet.
8.4.1.5 Alternative Approach
[0281] In an alternative embodiment, the order of these steps is
generally reversed to perform nucleic acid amplification followed
by an affinity-based assay that results in an optical or electrical
signal. In this sequence, an immunoassay would be performed to
monitor nucleic acid amplification.
8.4.2 Competitive iPCR
[0282] In one embodiment, the invention provides a competitive iPCR
performed on a droplet microactuator. Analytes for detection by
competitive iPCR are typically those that are too small for binding
two antibodies as required by a sandwich assay. In general, the
competitive iPCR involves: [0283] (1) immobilizing on a surface an
antibody with specificity for a target analyte; [0284] (2)
combining a sample droplet potentially including target analyte
with a droplet including a reporter analyte; [0285] (3) exposing
the immobilized antibody to the combined target analyte/reporter
analyte droplet so that the reporter analyte competes with any
target analyte for binding sites; [0286] (4) washing the substrate
to remove unbound analyte; [0287] (5) coupling the bound reporter
analyte to a reporter nucleic acid; and [0288] (6) amplifying the
reporter nucleic acid and monitoring the progress of the
amplification to determine the quantity of unbound reporter
analyte, which for the bound reporter analyte is inversely
proportional to the quantity of target analyte in the sample.
[0289] Any one or more of the foregoing steps can be performed
using droplet manipulation techniques on a droplet microactuator as
described herein. Each of the steps is discussed in further detail
in the ensuing sections.
8.4.2.1 Immobilizing Antibody
[0290] The antibody may be immobilized as described above in
Section 8.4.1.1.
8.4.2.2 Competitive Binding
[0291] A droplet including the sample potentially including a
target analyte is combined with a droplet including the reporter
analyte, and the combined droplet is brought into contact with the
immobilized antibody.
[0292] The reporter analyte may be made by coupling the reporter
nucleic acid to the analyte using any of a variety of conjugation
methods. In one embodiment, the analyte portion is modified with a
molecule, such as biotin, which generates a secondary capture site
for immobilizing a streptavidin-DNA complex. The coupling of biotin
to the analyte must not unduly interfere with its binding to the
primary capture antibody. The biotinylated material may in some
cases compete equally with the analyte from the sample. Coupling of
the biotinylated analyte to the reporter nucleic acid can occur
before or after the biotinylated analyte is captured by the
immobilized antibody.
[0293] For example, in one embodiment, the assay is performed by
mixing a droplet with a known quantity of biotinylated analyte with
the sample droplet potentially containing an unknown quantity of
unmodified analyte. A droplet including the biotinylated analyte is
combined with a droplet potentially including the target analyte.
The combined droplet is contacted with the immobilized antibody so
that the biotinylated analyte and the target analyte (if any)
compete for binding to the immobilized antibody. The quantity of
biotinylated analyte bound is inversely proportional to the
quantity of analyte in the sample droplet.
8.4.2.3 Coupling the Nucleic Acid Reporter
[0294] After washing, a droplet with a streptavidin-biotin-reporter
nucleic acid complex is added to a droplet including the washed
beads or surface. The streptavidin-biotin-reporter nucleic acid
complex binds to any biotinylated analyte that was captured by the
antibody on the bead.
8.4.2.4 Amplifying the Nucleic Acid
[0295] After washing, the quantity of a
streptavidin-biotin-reporter nucleic acid complex immobilized is
determined by amplification of the reporter nucleic acid. The
amplification signal is an inverse measure of the quantity of
analyte in the original sample. Amplification may proceed as
described in Section 8.1. The presence and quantity of amplified
product produced is measured, e.g., using real time fluorescence
detection. The quantity of reporter analyte that was displaced is
proportional to the quantity of target analyte in the sample.
8.4.2.5 Alternative Approaches
[0296] The steps are not limited to the order given. For example,
the antibody can be bound to the target analyte/reporter analyte
before it is immobilized by combining a droplet including the free
antibody with one or more droplets including the target
analyte/reporter analyte, after which the antibody may be brought
into contact with the surface for immobilization. The reporter
analyte may be conjugated with the reporter nucleic acid on the
droplet microactuator by combining droplets including the two
reagents. A droplet including the reporter analyte may be combined
with a droplet including the reporter nucleic acid to affect
conjugation before or after the reporter analyte is exposed to the
captured antibody. A variety of alternatives is possible within the
scope of the invention.
8.4.3 Samples and Sample Preparation
[0297] A wide variety of analytes may be detected using
droplet-based iPCR protocols of the invention. A single sample may
be analyzed for one or more target analytes. Analytes may, for
example, be biological analytes or synthetic analytes. For example,
in one embodiment, the analytes are selected from following
categories: analytes from bacterial sources, analytes from viral
sources, analytes from spore sources, protein toxin analytes, and
small molecule toxin analytes. In one embodiment, the target
analytes include toxins or analytes indicative of the presence of
specific biological organisms, e.g., infectious diseases, or toxins
that are employed in bioterrorism or biological warfare. Examples
of such organisms include anthrax, avian influenza, botulism,
hantavirus, legionnaires' disease, pneumonic plague, smallpox,
tularemia, and viral hemorrhagic fevers (VHFs).
8.4.4 Immuno-PCR Protocols
[0298] The system of the invention enables multiple immuno-PCR
tests to be simultaneously performed on a single sample. Further,
immuno-PCR tests may be performed along with other tests, such as
PCR and/or affinity-based assays.
[0299] The system provides multiplexed detection. In one
embodiment, the system has the ability to detect 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,
42, 43, 44, 45, 46, 47, 48, 49, 50 or more analytes. The analytes
may, for example, include analytes from natural or non-natural
sources. In another embodiment, the invention has the ability to
detect one or more analytes from any 2, 3, 4 or 5 the following
categories: analytes from bacterial sources, analytes from viral
sources, analytes from spore sources, protein toxin analytes, and
small molecule toxin analytes.
[0300] The system may be programmed to implement additional tests
as needed to increase confidence for a single target result.
Importantly, the droplet microactuator system can be programmed to
effect confirmatory re-testing of positives to reduce the
possibility of false positives. The system may also be programmed
and configured to permit storage of tested samples on the droplet
microactuator for subsequent additional laboratory testing.
[0301] In operation, the system performs analysis and provides
results extremely quickly. For example, in one embodiment, the
system has the ability to detect 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,
29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,
46, 47, 48, 49, 50 or more analytes in less than about 60, 50, 40,
30, 20, 15 or 10 minutes. In another embodiment, the system has the
ability to detect 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
50 or more analytes from any 2, 3, 4 or 5 the following categories:
analytes from bacterial sources, analytes from viral sources,
analytes from spore sources, protein toxin analytes, and small
molecule toxin analytes, and all tests are completed in less than
about 60, 50, 40, 30, 20, 15 or 10 minutes.
8.4.5 Applications
[0302] The iPCR assays provided by the invention are useful for
detecting a wide variety of molecules present in extremely small
quantities. Among other things, the system is useful for
surveillance for a chemical, biological or explosive threat. For
example, antibody to explosives can be used to detect the presence
of trace amounts of explosive in a sample. Thus, the invention also
provides a method of screening an area for chemical or biological
analytes indicative of the presence of biological, chemical, or
explosive weapons.
[0303] In one embodiment, iPCR technique is used to test a sample
for the presence of a biological organism, such as a bacteria or a
virus. In some embodiments, the system can achieve even
single-organism detection. Further, some embodiments may include
PCR bacterial typing or variance.
8.5 Analysis of Biological Fluids
[0304] The invention provides methods, devices and systems for
analysis of blood, various components of blood, and other
biological fluids. Illustrative designs for a biological fluid
analyzer are shown in FIGS. 9 and 17.
[0305] FIG. 9 illustrates one embodiment of a biological fluid
analyzer 900. In this embodiment, various modules may be provided
for conducting biological fluid analysis, such as, for example,
detection of metabolites (e.g., glucose, lactate, blood urea
nitrogen, and creatinine), electrolytes (e.g., K.sup.+, Cl.sup.-,
and Na.sup.+), proteins, and enzymes. These various modules may
include amperometric module 902, potentiometric module 904, optical
module 906, and conductometric module 908.
[0306] Another embodiment of a biological fluid analyzer 1700 is
illustrated in FIG. 17. In this embodiment, multiple fluid ports or
reservoirs may be provided such as antibody reservoirs 1701 (such
as for bacteria antibodies, spore antibodies, bacteria AB-DNA,
spore AB-DNA, protein toxin antibodies, small molecule antibodies,
protein AB-DNA, and small molecule SB-A DNA), PCR primer reservoirs
1702, and PCR reagents reservoirs 1703. Sample port 1704 may also
be provided, as well as sample reservoir 1705, wash solution area
1706, and waste reservoir 1707. Other areas that may be provided
include hot temperature area 1708, cold temperature area 1709, and
detector area 1710.
[0307] It will be appreciated that an important aspect of the
invention involves the ability to conduct droplet operations using
each of the required biological fluid analysis samples and reagents
on a droplet microactuator. For example, the invention includes:
[0308] (1) a droplet microactuator comprising thereon a droplet
comprising any one or more of the reagents and/or samples described
herein for conducting such biological fluid analysis; [0309] (2) a
device or system of the invention comprising such droplet
microactuator; [0310] (3) a method of conducting droplet operations
on or otherwise manipulating a droplet making use of such droplet
microactuator or system; and/or [0311] (4) a method of conducting
an droplet-based affinity-based assay making use of such droplet
microactuator or system.
[0312] For example, the droplet operations may include one or more
of the following: loading a droplet into the droplet microactuator;
dispensing one or more droplets from a source droplet; splitting,
separating or dividing a droplet into two or more droplets;
transporting a droplet from one location to another in any
direction; merging or combining two or more droplets into a single
droplet; diluting a droplet; mixing a droplet; agitating a droplet;
deforming a droplet; retaining a droplet in position; incubating a
droplet; heating a droplet; vaporizing a droplet; cooling a
droplet; disposing of a droplet; transporting a droplet out of a
droplet microactuator; other droplet operations described herein;
and/or any combination of the foregoing. Various other methods,
devices, systems, and other aspects of the invention will be
apparent from the ensuing discussion.
8.5.1 Sample and Sample Preparation
[0313] Examples of suitable samples for use with the droplet
microactuator of the invention include whole blood, serum, and
plasma, and various components thereof. Venous, arterial, or
capillary blood can be used. Examples of other samples usefully
analyzed according to the present invention include cerebrospinal
fluid (CSF), urine, saliva, sweat, tears, amniotic fluid, pleural
fluid, milk, cystic fluid, synovial fluid, stool, and semen.
[0314] Serum and/or plasma may be extracted from whole blood on the
droplet microactuator and/or prior to introduction into the droplet
microactuator. An example of a loading structure 1000 provided for
this purpose is provided in FIG. 10. In this embodiment, fluid is
flowed from a reservoir 1002 through a sealing means 1004 into a
loading chamber 1006 where it comes into contact with a membrane
1008. Permeate passes into a permeate flow channel 1010 through
which it flows into droplet microactuator reservoir 1012, assisted
by pressure source 1014 which applies pressure via channel
1016.
[0315] The small size of the device dramatically reduces the volume
of sample required for routine testing, which is an important
concern in many settings. For example, typical sample sizes will
have a volume which is in one embodiment from about 1 mL to about
100 mL, or about 10 mL to about 10 mL, or about 1 .mu.L to about 10
.mu.L.
8.5.2 Analytes
[0316] The invention provides a versatile droplet microactuator
system capable of performing an array of tests on a single
sub-microliter droplet of blood or any physiological sample of
about 0.5 .mu.L. Examples of suitable tests include metabolites
(e.g., glucose, creatinine, lactate, blood urea nitrogen),
electrolytes/elements (e.g., K.sup.+, Na.sup.+, Cl--, P, Mg, Li,
Ca, Fe), gases (e.g., pH, pCO.sub.2, NH.sub.3), enzymes (alkaline
phosphatase (ALP), aspartate aminotransferase (AST), alanine
aminotransferase (ALT), lactate dehydrogenase (LDH), Lipase,
Creatine Kinase, Creatine Kinase MB), proteins (albumin, c-reactive
protein (CRP), urine microalbumin, urine protein, cerebrospinal
fluid protein, serum total protein), and hematocrit. Other analytes
include glycated hemoglobin (Alc), hemoglobin, uric acid,
triglycerides, cholesterol, high density lipoprotein (HDL) and low
density lipoprotein (LDL).
8.5.2.1 Metabolites
[0317] The invention is useful in conducting a variety of
enzyme-coupled assays, such as for glucose, blood urea nitrogen,
creatinine, and lactate based on electrochemical or optical
detection. In some embodiments, glucose, lactate, and creatinine
are measured through the amperometric detection of H.sub.2O.sub.2
in an enzyme-coupled assay performed on the droplet
microactuator.
[0318] In some embodiments, the invention includes an
electrochemistry module with electrodes for amperometric and/or
potentiometric detection of metabolites (e.g., glucose, lactate,
blood urea nitrogen, creatinine).
8.5.2.2 Electrolytes
[0319] For quantifying various ions (e.g., ammonia, bromide,
cadmium, calcium, chloride, copper, cyamide, fluoride, fluorborate,
iodide, lead, nitrate, perchlorate, potassium, silver/sulfide,
magnesium, iron, lithium, phosphorus, sodium, surfactant,
thiocyanate) in a sample, such as a processed biological sample,
the droplet microactuator may be modified to include an
ion-selective electrode (ISE). A sample droplet may be transported
into contact with the ISE for detection of the desired ion.
Further, prior to detection, standard droplets may be brought into
contact with the ISE for the purpose of calibration. In some
embodiments, the invention includes an electrochemistry module with
electrodes for amperometric, potentiometric, and/or conductometric
detection of electrolytes (e.g., K.sup.+, Cl.sup.-, Na.sup.+).
[0320] ISEs can be included in the droplet microactuator for
detecting electrolytes. ISEs can, for example, be included as
components of a top and/or bottom substrate and/or as components
exposed to a space between a top and/or bottom substrate or
associated with a single substrate droplet microactuator. They can
be integrated with transport electrodes. The ISEs are generally
arranged so that droplet operations can be employed to bring a
droplet on the droplet microactuator into contact with an ISE.
Various techniques can be used to make ion selective electrodes on
the droplet microactuator. Examples include screen printing, as
well as photolithography, etching, and lift-off.
[0321] As a specific non-limiting example, Ag/AgCl can be screen
printed to provide working and reference electrodes with a KCl salt
bridge. Examples of suitable ionophores in PVC for the fabrication
of ion-selective membranes include methyl monensin for Na.sup.+,
valinomycin for K.sup.+, quaternary ammonium chloride for Cl--, and
tridodecyl amine for pH. The ion-selective membranes can be made by
micro dispensing and/or spray-coating (e.g., thermal/ultrasonic
printing).
[0322] Electrolytes can be detected in any biological sample.
Specific non-limiting examples include whole blood, plasma and
serum, as well as the examples provided elsewhere in this
disclosure.
8.5.2.3 Gases
[0323] For quantifying the presence of gasses (e.g., pCO.sub.2,
PO.sub.2) or pH, various specialized electrodes may be used. As a
non-limiting example, a carbon dioxide microprobe may be
incorporated into a droplet microactuator of the invention for
detection and/or quantification of carbon dioxide. The microprobe
may be arranged so that droplet operations can be employed to bring
a droplet on the droplet microactuator into contact with the
microprobe. Further, prior to detection, standard droplets may be
brought into contact with the carbon dioxide microprobe, using
droplet operations, for the purpose of calibration. Corresponding
approaches are suitable for detecting oxygen and/or determining pH.
In some embodiments, the droplet microactuator may include
electrodes for amperometric, potentiometric, and/or conductometric
detection of blood gases (e.g., pCO.sub.2, pO.sub.2, pH).
[0324] As a specific non-limiting example, a Severinghaus-type
CO.sub.2 sensor can be made with the pH electrode made of
gold-quinhydrone electrode immersed with the internal solid
electrolyte made of NaHCO.sub.3, NaCl, and a sucrose binder. A gas
permeable membrane of polydimethylsiloxane can be deposited
thereon. Digital conditioning electronics (e.g., high input
impedance amplifiers) can be used to interface with the
potentiometric electrodes.
[0325] Gasses can be detected in any droplet on the droplet
microactuator. Specific non-limiting examples include droplets
including whole blood, plasma, and/or serum, as well as the
biological samples described elsewhere in this disclosure.
8.5.2.4 Enzyme
[0326] In some embodiments, the invention includes
chemiluminescence assays for detection of enzymes, such as liver
enzymes. Using a series of droplet-based multiple enzymatic steps,
the ALT and AST assays can be reduced to a final step that produces
hydrogen peroxide which can be measured quantitatively by
absorbance, luminescence, fluorescence, or electrochemically.
8.5.2.5 Serum Protein
[0327] A colorimetric assay may be utilized for detection of total
protein in a sample. Examples of suitable calorimetric methods
include: the Biuret method, the Lowry method, the bicinchoninic
acid (BCA) assay, and Bradford assay. The Biuret method generally
involves contacting a sample droplet with a droplet comprising
cupric ions. The cupric ions form a colored complex with proteins.
The Lowry reaction approach is based on the amplification of the
biuret reaction by combining with a Folin reagent droplet. A
variation of the Lowry assay uses a Bicinchoninic acid (BCA)
droplet to permit detection of the cuprous ions generated from
cupric ions by reaction with protein in a droplet under alkaline
conditions. The Bradford assay approach involves combining the
sample with a droplet comprising Coomassie Blue dye to form a
colored complex. In each case, an LED/photodiode setup, e.g., as
shown in FIG. 21A, can be used for monitoring the absorbance. Total
protein can be detected in any sample droplet using techniques
described herein, including optical sensing methods based on
fluorescence and/or chemiluminescence, as well as using the
affinity-based assay techniques disclosed herein. Specific
non-limiting examples of useful samples for determining total
proteins include biological samples, such as whole blood, plasma
and serum, as well as the samples described elsewhere in this
disclosure.
8.5.2.6 Hematocrit
[0328] Red blood cells can be quantified in a sample droplet using
a variety of techniques. For example, the hemoglobin content can be
calculated by measuring absorbance at 805 nm. Oxyhemoglobin can
then be calculated by measuring the absorbance at 650 nm. Results
may be obtained by comparing the absorbance measurements for
samples to the absorbance measurements for a series of known
standards.
[0329] In some embodiments, the invention includes an
electrochemistry module with electrodes for amperometric,
potentiometric, and/or conductometric detection of hematocrit. The
droplet microactuator may include a conductometric cell with a pair
of electrodes for AC conductometric measurement of hematocrit. For
a two-substrate droplet microactuator, the electrodes may be
located on one or both substrates. The electrodes are arranged so
that arranged so that droplet operations can be employed to bring a
droplet on the droplet microactuator into contact with the
electrodes.
8.5.3 Multi-Analyte Analyzer
[0330] Examples of suitable analytes are glucose, creatinine,
lactate, BUN, K.sup.+, Na.sup.+, Cl.sup.-, pH, pCO.sub.2, ALP,
total protein, and hematocrit. In one embodiment, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12 or more analytes are analyzed on a single droplet
microactuator. Preferably, these analytes are selected from
glucose, creatinine, lactate, BUN, K.sup.+, Na.sup.+, Cl.sup.-, pH,
pCO.sub.2, ALP, total protein, and hematocrit. In one embodiment,
glucose, creatinine, lactate, BUN, K.sup.+, Na.sup.+, Cl.sup.-, pH,
pCO.sub.2, ALP, total protein, and hematocrit are analyzed on a
single droplet microactuator. Other examples of suitable analytes
include calcium, bilirubin, albumin, clotting time, ALT, and
AST.
[0331] In some embodiments, assays 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12 or more analytes are processed in parallel on a droplet
microactuator system of the invention, i.e., one or more processing
and/or detecting steps for such analyte are accomplished
simultaneously with one or more processing and/or detecting steps
for another analyte on a single droplet microactuator. A droplet
microactuator system may execute 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
or more colorimetric assays for detection of the same or different
analyte types in parallel. The droplet microactuator system may
execute 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more
chemiluminescence assays for detection of the same or different
analyte types in parallel. The droplet microactuator may execute 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more amperometric assays for
detection of the same or different analyte types in parallel. The
droplet microactuator may execute 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12 or more potentiometric assays for detection of the same or
different analyte types in parallel. The droplet microactuator may
execute 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more fluorescence
assays for detection of the same or different analyte types in
parallel. The droplet microactuator may include 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12 or more conductometric assays for detection of the
same or different analyte types run in parallel. The droplet
microactuator will include droplets or reservoirs including
reagents for executing each of the protocols. The droplet
microactuator device and/or system will include detection
components as needed for executing detection steps of the
protocols.
[0332] Moreover, the droplet microactuator may include 2, 3, 4, 5,
6, 7, 8, 9, 10, 11, 12 or more analytes that are processed in
parallel, and the system may execute 1, 2, 3, 4, 5, 6 or more assay
protocols on these analytes. The droplet microactuator may include
2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more analytes that are
processed in parallel, and execute 1, 2, 3, 4, 5, 6 or more assay
protocols on these analytes, where the assays are selected from
colorimetric assays, chemiluminescence assays, fluorescence assays,
amperometric assays, potentiometric assays and conductometric
assays. The droplet microactuator will include droplets or
reservoirs including reagents for executing each of the protocols.
The droplet microactuator device and/or system will include
detection components as needed for executing detection steps of the
protocols.
[0333] Furthermore, various protocols for nucleic acid
amplification, nucleic acid sequencing, affinity-based assays, cell
handling, bead handling and washing, and analyte detection
protocols may also be readily integrated into a single droplet
microactuator system. In one embodiment, a single droplet
microactuator includes reagents and detection components for
conducting nucleic acid amplification and nucleic acid sequencing.
In another embodiment, a single droplet microactuator includes
reagents and detection components to conduct nucleic acid
amplification for detection of a blood-borne pathogen and reagents
and detection components for conducting one or more other assays
from those assay types and/or for analyte types as described
herein. In another embodiment, a droplet microactuator includes
components for manipulating cells along with components and
reagents for conducting affinity-based assays.
[0334] In short, the invention enables a droplet microactuator
system that not only performs the routine operations of a central
lab-based chemistry analyzer at higher throughput with dramatically
lower sample volumes, but also offers better functionality by
integrating hematology, pathology, molecular diagnostics, cytology,
microbiology, and serology onto the same platform.
[0335] In one embodiment, the invention provides a droplet
manipulation module integrated with an optical detection module and
an electrochemical detection module for analyzing blood gases,
electrolytes, enzymes, proteins, and metabolites.
[0336] One embodiment of the invention employs a modular design to
partition independently optimized fabrication processes. For
example, all the electrochemical components can be fabricated on a
substrate, all the microfluidic electrodes can be fabricated on
another substrate, and all the electronics can be fabricated on yet
another substrate. A disposable sandwich droplet microactuator can
be formed between the electrochemical module and the droplet
manipulation module which can be coupled to a reusable electronics
module for data acquisition and analysis. Optical detection modules
can be constructed in the analyzer.
8.5.4 Biological Fluid Analysis Detection
[0337] The biological fluid analyses described herein make use of a
variety of detection approaches, e.g., as described in Sections
8.1, 8.2, 8.3, 8.4, 8.5, and 8.11.
8.6 Surfaces and Surface Washing Protocols
[0338] Various protocols of the invention require surfaces for
immobilization of reactants. For example, surfaces may be used to
capture or immobilize target components of a droplet, such as
cells, other beads, microparticles, nanoparticles, antibodies,
proteins, peptides, nucleic acids, small molecules and/or other
chemical components. Surfaces used for such purposes may, for
example, include surfaces of beads, microparticles, nanoparticles,
membranes, physical objects, and/or droplet microactuator surfaces.
Various protocols require washing step in which unbound materials
are removed from one or more surfaces.
[0339] A sample droplet including one or more target components for
capture may, using droplet operations, be contacted with a surface
having affinity for such targets. Washing protocols of the
invention may be used to remove from the surface unbound components
of the sample droplet. For example, a droplet protocol may be used
to bring one or more droplets including one or more target
components into contact with one or more surfaces so that the one
or more target components may be immobilized or captured on the one
or more surfaces. A washing protocol may be executed to remove
unbound substances from the one or more surfaces. Similarly, a
droplet protocol may be used to bring one or more droplets
including one or more target components into contact with one or
more beads so that the one or more target components may be
immobilized or captured on the one or more beads. A washing
protocol may be executed to separate unbound substances from the
one or more beads.
[0340] Washing generally involves bringing one or more washing
droplets into contact with the immobilized surface. Washing may
involve agitation of the droplets while in contact with the
surface. Washing droplets may, for example, include water,
deionized water, saline solutions, acidic solutions, basic
solutions, detergent solutions and/or buffers.
[0341] Washing protocols of the invention result in highly
efficient removal of unbound substances from the surface. In one
embodiment, the invention provides method of providing a droplet in
contact with a surface with a reduced concentration of a substance.
This method may generally include providing a surface in contact
with a droplet comprising a starting concentration of the substance
and having a starting volume; conducting one or more droplet
operations to merge a wash droplet with the droplet to yield a
combined droplet; and conducting one or more droplet operations to
divide the combined droplet to yield a set of droplets including:
(i) a droplet in contact with the surface having a decreased
concentration and decreased quantity of the substance relative to
the starting concentration; and (ii) a droplet which is separated
from the surface.
[0342] The method of the invention may yield a droplet in contact
with the surface having a decreased quantity or substantially
decreased quantity of the substance relative to the starting
concentration. The resulting droplet may in some embodiments have a
volume which is approximately the same as the starting volume. In
some embodiments, the washing steps may be repeated until a
predetermined maximum quantity of the one or more components is met
or exceeded in the resulting droplet. The predetermined amount may
represent a substantial reduction relative to the starting
concentration. In some cases, the resulting droplet may be
substantially free of the components. For example, in some
embodiments, the reduction in amount exceeds 99, 99.9, 99.99,
99.999, 99.9999, 99.99999, 99.999999 percent on a molar basis.
[0343] The method of the invention may yield a droplet in contact
with the surface having a decreased concentration or substantially
decreased concentration of the substance relative to the starting
concentration. The resulting droplet may in some embodiments have a
volume which is approximately the same as the starting volume. In
some embodiments, the washing steps may be repeated until a
predetermined maximum concentration of the one or more components
is met or exceeded in the resulting droplet. The predetermined
concentration limit may represent a substantial reduction relative
to the starting concentration. In some cases, the resulting droplet
may be substantially free of the components. For example, in some
embodiments, the reduction in concentration exceeds 99, 99.9,
99.99, 99.999, 99.9999, 99.99999, 99.999999 percent.
8.6.1 Washing Beads
[0344] For protocols making use of beads, droplet with beads can be
combined using droplet operations with one or more wash droplets.
Then, while retaining the beads (e.g., physically or magnetically),
the merged droplet may be divided using droplet operations it into
two or more droplets: one or more droplets with beads and one or
more droplets without a substantial amount of beads. In one
embodiment, the merged droplet is divided using droplet operations
into one droplet with beads and one droplet without a substantial
amount of beads.
[0345] Generally, each execution of a washing protocol results in
retention of sufficient beads for conducting the intended assay
without unduly detrimental effects on the results of the assay. In
certain embodiments, each division of the merged droplet results in
retention of more than 90, 95, 97, 98, 99, 99.1, 99.2, 99.3, 99.4,
99.5, 99.6, 99.7, 99.8, 99, 99.9, 99.99, 99.999, 99.9999, 99.99999,
or 99.999999 percent of beads. In other embodiments, each execution
of a washing protocol to achieve a predetermined reduction in the
concentration and/or amount of removed substance results in
retention of more than 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6,
99.7, 99.8, 99, 99.9, 99.99, 99.999, 99.9999, 99.99999, or
99.999999 percent of beads. In still other embodiments, the amount
of retained beads is calculated and the results are adjusted
accordingly.
[0346] In some embodiments, beads can be washed in reservoirs in
which the bead-containing droplet and wash droplets are combined,
beads are retained (for example by a magnet, by physical
structures, electrostatic forces), and droplets lacking beads are
dispensed from the reservoir using droplet operations. For example,
beads can be washed by dilute-and-dispense strategy whereby a wash
buffer is added to the reservoir to dilute the contents,
magnetically responsive beads are localized within the reservoir
with a magnet and most of the solution is dispensed from the
reservoir, and this cycle is repeated till acceptable levels of
washing are achieved.
8.6.1.1 Washing Magnetically Responsive Beads
[0347] A non-limiting example, illustrated in FIG. 11, involves
immobilizing magnetically responsive beads using a magnetic field.
Immobilized magnetically responsive beads may be freed by reduction
or elimination of the magnetic field. Washing magnetically
responsive beads may generally include the following steps: [0348]
(1) using droplet operations to position a droplet 1101 comprising
magnetically responsive beads 1102 and unbound substances 1103 in
proximity with a magnet 1104; [0349] (2) using droplet operations
to combine a wash droplet 1106 with the droplet 1101 comprising the
magnetically responsive beads 1102; [0350] (3) immobilizing the
beads 1102 by application of a magnetic field; [0351] (4) using
droplet operations to remove some or all of the droplet surrounding
the beads to yield a droplet 1108 comprising the beads with a
reduced concentration of unbound target substance and a droplet
1110 comprising unbound target substance; [0352] (5) releasing the
beads 1102 by removing the magnetic field; [0353] (6) repeating
steps (2) to (3) or (2) to (4) until a predetermined degree of
purification is achieved.
[0354] In this manner, unbound substances, such as contaminants,
byproducts or excess reagents, can be separated from the beads.
Each cycle produces a droplet including the beads but with a
decreased level of the unwanted substances. Step (5) is not
required in each washing cycle; however, it may be useful to
enhance washing by freeing contaminants which may be trapped in the
immobilized beads. Steps may be performed in a different order,
e.g., steps (2) and (3) may be reversed. Steps in the washing
protocol may be accomplished on a droplet microactuator using
droplet operations as described herein.
[0355] Another embodiment is illustrated in FIG. 12 and may
comprise a top plate 1201, bottom plate 1202, electrodes 1203, and
a magnet 1204. The embodiment steps generally may include: [0356]
(1) using droplet operations to combine a slug 1205 with a droplet
1206 comprising magnetically responsive beads 1207 and unbound
material 1208 in proximity with magnet 1204; [0357] (2,3) with the
beads 1207 immobilized, using droplet operations to transport the
resulting combined slug 1210 across the beads 1207 to separate
unbound material 1208 from the beads 1207; [0358] (4) using droplet
operations to separate off a portion of the combined slug 1210 to
yield a portion 1212 comprising the beads with a reduced
concentration of unbound target substance and a portion 1214
comprising unbound target substance; [0359] (5) repeating steps
(1)-(4) as needed to achieve the desired reduction in unbound
material.
[0360] In a related approach, the slug may be continuously
supplemented by adding additional wash droplets and/or slugs as the
slug is being transported across the immobilized beads. The process
may continue until the desired reduction in unbound material is
achieved.
[0361] FIG. 13 illustrates an alternative embodiment which may also
comprise a top plate 1301, bottom plate 1302, electrodes 1303, and
a magnet 1304. In this embodiment, the magnet 1304 is moved, such
as in the direction of Al, to separate beads 1305 from unbound
material 1306 in a combined slug 1307 rather than moving the slug
1307. A similar approach involves movement of both the magnet and
the slug to achieve separation (not shown). Yet another approach
involves using multiple magnets to move the beads (not shown).
[0362] In embodiments in which magnetically responsive beads are
used, the inventors have found that application of a magnetic field
though useful for temporarily immobilizing beads, moving beads
and/or positioning beads, sometimes results in unwanted aggregation
of the beads. In one embodiment, a surfactant is included to
prevent or reduce bead aggregation. Examples of surfactants
suitable for this purpose include: Tween.RTM. 20, Tween.RTM. 80,
Triton X-100. Surfactants should be selected and used in amounts
which reduce or eliminate bead aggregation and minimize
non-specific adsorption while at the same time not resulting in
significant loss of target analytes or reagents from the
droplet.
[0363] Another approach to eliminating or reducing clumping
aggregation of beads involves the use of smaller numbers of larger
beads. Any number of beads which can be contained in a droplet
during one or more droplet operations may be used. In some
embodiments, the number of magnetically responsive beads can range
from 1 to several 100,000's. For example, in one embodiment, the
invention makes use of one to 100 magnetically responsive beads per
droplet. For example, the invention may make use of 1, 2, 3, 4, 5,
6, 7, 8, 9, 10 . . . 100 magnetically responsive beads per droplet.
In one embodiment, the number of magnetically responsive beads is
from one to 10. Use of smaller numbers of magnetically responsive
beads permits larger beads to be used. For example, in one
embodiment, the invention makes use of one to 100 magnetically
responsive beads per droplet, where the beads have an average
diameter of about 25 to about 100 microns. In another embodiment
the invention makes use of one to 10 magnetically responsive beads
per droplet, where the beads have an average diameter of about 50
to about 100 microns.
8.6.1.2 Washing Non-Magnetically Responsive Beads
[0364] A similar approach may be used with beads that are not
magnetically responsive or not significantly magnetically
responsive. As illustrated in FIG. 14, instead of using a magnetic
field to immobilize beads 1401, a physical obstacle 1402 may be
used to permit removal of some or all of droplet 1403 surrounding
the beads 1401. The physical obstacle 1402 may, for example,
include a membrane, sieve, and/or projection from the droplet
microactuator (e.g., from the top plate 1404 and/or bottom plate
1405). Where a physical obstacle 1402 (projection or object)
attached to the top plate 1404 and/or bottom plate 1405 is
employed, it should be arranged so as to permit transport using one
or more adjacent electrodes 1406 while preventing the beads 1401
from following, e.g., using a projection from the top plate that
leaves sufficient space for droplet transport and/or a projection
with one or more openings that permits the droplet to be
transported through the opening while preventing the beads from
following.
8.6.2 Washing Droplet Microactuator Surfaces
[0365] FIG. 15 illustrates an example of an approach for washing a
droplet microactuator surface. In this non-limiting example, a
surface 1501 is located on the interior of the top plate 1502. In
this approach, (1) a sample droplet 1503 including a target
substance 1504 having affinity for a surface component 1505 is
(using droplet operations) brought into contact with the surface
1501, causing (2) some portion or all of the target substance to be
immobilized. (3) A wash droplet 1506 and the sample droplet 1503
are combined using droplet operations to yield a combined
wash-sample droplet 1507. (4) The combined wash-sample droplet is
then divided using droplet operations to yield a portion 1508 in
contact with the surface and comprising a reduced concentration of
unbound target substance and a portion 1509 separated from the
surface comprising unbound target substance. Steps (3) and (4) may
be repeated as needed to achieve the desired reduction in unbound
material.
8.7 Cell Handling
[0366] Various protocols of the invention may make use of droplets
including cells. The droplets may include culture media for
maintaining cell viability and/or growing cell cultures. In some
cases, the invention makes use of droplets having predetermined
numbers of cells. For example, in some embodiments, the invention
may make use of droplets including single cells. For example,
droplets with single cells may be useful to product clonally pure
cell populations and/or to conduct experiments studying the
reaction of single cells to specific stimuli. Droplets with
predetermined numbers of cells may be provided by dispensing
droplets from a cell suspension onto a droplet transport pathway or
network from a suspension of cells and/or by dividing droplets with
multiple cells into one or more subdroplets. The suspension may be
supplied from an external source or may be stored in a droplet
microactuator reservoir. Droplets can be analyzed to determine the
number of cells in each droplet, and droplets with a preselected
number of cells can be routed downstream for further processing.
Dispensed droplets with multiple cells may themselves be combined
with one or more buffer droplets and divided into two or more
sub-droplets and analyzed for the presence of single cells.
[0367] Sort decisions can be based on droplet analysis. For
example, light transmission may be used to identify droplets with a
predetermined number of cells. Sort decisions may be made based on
the measurement of transmitted light. Other embodiments may employ
automated image analysis and/or or multi-color fluorescence and/or
scattering analysis. Droplets not meeting specifications can be
reintroduced into the sample reservoir for another attempt or
transported to a waste reservoir.
[0368] Droplets meeting cell count specifications may be
transported to droplet microactuator reservoirs and/or transported
for sorting and/or enrichment. One approach to providing reservoirs
with enriched cell content is illustrated in FIGS. 16A and 16B. In
this embodiment, droplets 1602 are dispensed from a cell suspension
1604 and transported based on their characteristics to reservoirs
1606 on droplet microactuator 1600.
[0369] In other embodiments, droplets may be further manipulated,
e.g., as discrete droplets for analysis of the cells contained
within. Droplets including predetermined numbers of cells may be
used as inputs for various assay protocols described herein. In
some embodiments, gravity is not used as the motive force for
transporting droplets.
[0370] In one specific embodiment, tumor cells may be isolated on
the droplet microactuator. Cells may, for example, be isolated from
microliters of fine-needle aspirates (FNA). In another embodiment,
samples such as blood stem cells, bone marrow, GI washes, and
cryopreserved-thawed samples can be analyzed for cancer cells.
[0371] Immunogenic capture of relevant cells can be accomplished
using antibody beads, such as anti-cytokeratin beads, may be used
to capture relevant cells from a sample prior to introduction into
the droplet microactuator and/or from a droplet on a droplet
microactuator. Binding may be enhanced or incubation times reduced
on the droplet microactuator by actively shuttling the droplet or
vortexing the droplet within a reservoir. Beads can be isolated and
washed as described elsewhere herein. Target cells can be released
into suspension in a droplet on the droplet microactuator.
[0372] Uniform numbers of cells per droplet from can be dispensed
from an on-chip reservoir using cell dispensing approaches
described herein. Droplets with cells can be aliquoted into
multiple on-chip reservoirs. Cells can be incubated in on-chip
reservoirs. Cell viability can be assessed, e.g., using resazurin
as a fluorescent redox indicator. Living cells convert the
non-fluorescent resazurin dye into resorufin which fluoresces red.
Non viable cells do not fluoresce. Cells can be distributed to
on-chip reservoirs and nucleic acid from the cells can be amplified
using approaches as described herein.
8.8 Droplet Microactuator Architecture and Operation
[0373] The system of the invention generally includes a droplet
microactuator controlled by a processor. For example, the processor
may, among other things, be programmed to control droplet
manipulations on a droplet microactuator. A wide variety of droplet
microactuator configurations is possible. Various illustrations are
provided in FIGS. 1, 2, 6, 9, and 17. Examples of components which
may be configured into a droplet microactuator of the invention
include various filler fluids which may be loaded on the droplet
microactuator; fluid loading mechanisms for introducing filler
fluid, sample and/or reagents onto the droplet microactuator;
various reservoirs, such as input reservoirs and/or processing
reservoirs; droplet dispensing mechanisms; means for controlling
temperature of the droplet microactuator, filler fluid, and/or a
droplet on a droplet microactuator; and magnetic field generating
components for manipulating magnetically responsive beads on a
droplet microactuator. This section discusses these and other
aspects of the droplet microactuator and their use in the systems
of the invention.
8.8.1 Droplet Microactuator
[0374] The systems make use of a droplet microactuator. The droplet
microactuator will include a substrate with one or more electrodes
arranged for conducting one or more droplet operations. In some
embodiments, the droplet microactuator will include one or more
arrays, paths or networks of such electrodes. A variety of
electrical properties may be employed to effect droplet operations.
Examples include electrowetting and electrophoresis.
[0375] In one embodiment, the droplet microactuator includes two or
more electrodes associated with a substrate, and includes a means
for permitting activation/deactivation of the electrodes. For
example, the electrodes may be electronically coupled to and
controlled by a set of manual switches and/or a controller. The
droplet microactuator is thus capable of effecting droplet
operations, such as dispensing, splitting, transporting, merging,
mixing, agitating, and the like. Droplet manipulation is, in one
embodiment, accomplished using electric field mediated actuation.
Electrodes will be electronically coupled to a means for
controlling electrical connections to the droplet
microactuator.
[0376] The basic droplet microactuator includes a substrate
including a path or array of electrodes. In some embodiments, the
droplet microactuator includes two parallel substrates separated by
a gap and an array of electrodes on one or both substrates. One or
both of the substrates may be a plate. One or both substrates may
be fabricated using PCB, glass, and or semiconductor materials as
the substrate. Where the substrate is PCB, the following materials
are examples of suitable materials: Mitsui BN-300; Arlon 11N; Nelco
N4000-6 and N5000-30/32; Isola FR406, especially IS620;
fluoropolymer family (suitable for fluorescence detection since it
has low background fluorescence); polyimide family. Various
materials are also suitable for use as the dielectric component of
the substrate. Examples include: vapor deposited dielectric, such
as parylene C (especially on Glass), and parylene N; Teflon AF;
Cytop; and soldermasks, such as liquid photoimageable soldermasks
(e.g., on PCB) like Taiyo PSR4000 series, Taiyo PSR AUS series
(good thermal characteristics for applications involving thermal
control), and Probimer 8165 (good thermal characteristics for
applications involving thermal control); dry film soldermask, such
as those in the Dupont Vacrel family; and film dielectrics, such as
polyimide film (Kapton), polyethylene, and fluoropolymers like FEP,
PTFE. Some or all of the substrate may also include a hydrophobic
coating. Suitable examples include Teflon AF; Cytop; coatings in
the Fluoropel family; silane coatings; fluorosilane coatings; and
3M Novec electronic coatings.
[0377] Were the droplet microactuator includes two plates, droplets
may be interposed in the space between the plates. Space
surrounding the droplets typically includes a filler fluid. The
droplet microactuator can conduct droplet operations using a wide
variety of fluid droplets, though conductive fluids are
preferred.
[0378] Surfaces of the droplet microactuator are typically coated
with a hydrophobic coating. For applications involving thermal
cycling, a hydrophobic coating should be selected that is resistant
to thermal stress during prolonged thermocycling operation.
Examples of suitable thermal resistant materials include
soldermasks such as Probimer.RTM. 8165 which has been developed for
use in the automotive industry and has excellent thermal shock
resistance, and PCB board materials such as Mitsui BN-300 which is
resistant to high temperature and warpage.
[0379] Droplet transport occurs along a path or network of control
electrodes. The array or path includes electrical connections for
electrically coupling electrodes to external circuitry. The array
or path may also include electrical connections for electrically
coupling certain electrodes together. The electrodes are controlled
via the external circuitry by a processor. Droplet operations may
be effected by supplying voltage to the electrodes. While the
preferred voltage varies depending on the thickness of the
dielectric, for a dielectric constant in the range of 2-100 and
thickness in the range of 1 nm to 10 mm, the preferred energy per
unit area limits are in the range of about 300 microjoule/sq meter
to about 300000 microjoule/sq meter. The preferred activation
voltage is in the range of about 1 mV to about 50 kV, or about 1V
to about 10 kV, or about 5V to about 1000 V, or about 10V to about
300V.
[0380] Typically, the electrodes are fired via a voltage relay. The
droplet microactuator operates by direct manipulation of discrete
droplets, e.g., using electrical fields. For example, a droplet
adjacent to an energized electrode with surrounding electrodes
grounded will transport to align itself with the energized
electrode, i.e., the droplet will be transported to the position of
that electrode. A series of successive transfers will transport
droplets along the path or network of control electrodes. In
addition to transport, other operations including merging,
splitting, mixing and dispensing of droplets can be accomplished in
the same manner by varying the patterns of voltage activation.
[0381] It should be noted that electrodes can be activated in a
variety of ways. For example, an electrode can be activated by
applying a DC potential. Similarly, an electrode can be activated
by applying an AC potential, so that the activated electrode has an
AC potential an unactivated electrode has a ground or other
reference potential. In another aspect, the potential may be
applied by repeatedly activating an electrode and then inverting
it. An AC mode can be effected by using software to rapidly switch
between polarities of the outputs.
[0382] In some embodiments the invention employs droplet operation
structures and techniques described in U.S. Pat. No. 6,911,132,
entitled "Apparatus for Manipulating Droplets by
Electrowetting-Based Techniques," issued on Jun. 28, 2005 to Pamula
et al.; U.S. patent application Ser. No. 11/343,284, entitled
"Apparatuses and Methods for Manipulating Droplets on a Printed
Circuit Board," filed on Jan. 30, 2006; U.S. Pat. Nos. 6,773,566,
entitled "Electrostatic Actuators for Microfluidics and Methods for
Using Same," issued on Aug. 10, 2004 and 6,565,727, entitled
"Actuators for Microfluidics Without Moving Parts," issued on Jan.
24, 2000, both to Shenderov et al.; U.S. Patent Publication No.
20060254933, entitled "Device for transporting liquid and system
for analyzing" published on Nov. 16, 2006 by Adachi et al., the
disclosures of which are incorporated herein by reference for their
teachings concerning structures and techniques for conducting
droplet operations.
[0383] Droplet operations can be rapid, typically involving average
linear velocities ranging from about 0.01 cm/s to about 100 cm/s,
or from about 0.1 cm/s to about 10 cm/s, more preferably from about
0.5 cm/s to about 1.5 cm/s. Moreover, droplets may typically be
manipulated at a frequency of manipulation ranging from about 1 Hz
to about 100 KHz, preferably from about 510 Hz to about 10 KHz,
more preferably from about 25 Hz to about 100 Hz. In addition to
being rapid, droplet manipulations using the droplet microactuator
are also highly precise, and multiple droplets can be independently
and simultaneously manipulated on a single droplet
microactuator.
[0384] Discrete droplet operations obviate the necessity for
continuous-flow architecture and all the various disadvantages that
accompany such an architecture. For example, near 100% utilization
of sample and reagent is possible, since no fluid is wasted in
priming channels or filling reservoirs. Further, as noted above,
droplet movement can be extremely rapid. The droplet microactuator
may in some cases be supplemented by continuous flow components and
such combination approaches involving discrete droplet operations
and continuous flow elements are within the scope of the invention.
Continuous flow components may be controlled by the controller.
Nevertheless, in certain other embodiments, various continuous flow
elements are specifically avoided in the droplet microactuator of
the invention and/or methods of the invention. For example, in
certain embodiments, one or more of the following components is
excluded from a droplet microactuator and/or methods of the
invention: microchannels; fixed microchannels; networks of
microchannels; pumps; external pumps; valves; high-voltage
supplies; centrifugal force elements; moving parts.
[0385] Electric field mediated actuation also obviates the need for
other droplet operations and all the various disadvantages that
accompany such techniques. It will be appreciated that the droplet
microactuator may nevertheless be complemented or supplemented with
other droplet manipulation techniques, such as electrical (e.g.,
electrostatic actuation, dielectrophoresis), magnetic, thermal
(e.g., thermal Marangoni effects, thermocapillary), mechanical
(e.g., surface acoustic waves, micropumping, peristaltic), optical
(e.g., opto-electrowetting, optical tweezers), and chemical means
(e.g., chemical gradients). When these techniques are employed,
associated hardware may also electronically coupled to and
controlled by the controller. However, in other embodiments, one or
more of these droplet operation techniques is specifically excluded
from a droplet microactuator of the invention.
[0386] The droplet microactuator can be manufactured in a highly
compact form and can be driven using a very small apparatus. For
example, droplet microactuator and apparatus may together be as
small as several cubic inches in size. The droplet microactuator
requires only small amounts of electrical power and can, for
example, readily be operated using batteries. The droplet
microactuator can perform droplet operations using extremely small
droplets. Droplets are typically in the range of from about 1 fL to
about 1 mL, more preferably from about 100 pL to about 1 .mu.L,
still more preferably from about 10 mL to about 1 .mu.L.
[0387] The use of discrete droplets for on-chip processing instead
of continuous flows provides several important advantages. Since
sample fluid need not be expended for priming of channels or pumps
virtually all of the sample fluid can be used for analysis and very
small volumes of sample (e.g., less than about 100 .mu.L or less
than about 50 .mu.L or less than about 25 .mu.L) can be analyzed.
The same advantages apply to the use of reagents where reducing the
volume of reagents consumed has the advantage of reducing the cost
of the analysis. The use of discrete small-volume droplets also
permits a large number of reactions to performed in a small
footprint (e.g. greater than 10 per cm.sup.2 or greater than 100
per cm.sup.2 or greater 1,000 per cm.sup.2 or greater than 10,000
per cm.sup.2).
[0388] Various components of the invention may be included as
components of the droplet microactuator. In fact, an entire system
of the invention may be provided as an integrated droplet
microactuator. In some embodiments, the droplet microactuator
includes various sensors and means for electronically coupling the
sensors to external circuitry. In other embodiments, the droplet
microactuator includes heaters and/or magnetic field generating
elements and means for coupling such elements to external
circuitry. Further, a droplet microactuator including any one or
more of the reagents described herein in a reservoir or in droplet
form is also an aspect of the invention.
[0389] Optical windows can be patterned in the electrodes to
enhance the capability of performing optical detection on the chip.
Where the electrode is formed in an opaque material on a
transparent substrate, a window in the electrode can be created
permit light to pass through the substrate. Alternatively, when the
electrode material is transparent, a mask can be created to
eliminate stray light. Additionally, the opening can be patterned
as a diffraction grating. Adaptive optical windows can be created
as well, using a second electrowetting layer. For example, opaque
oil (e.g. oil dyed black) can be used with a transparent droplet to
create an temporary and movable optical window.
8.8.2 Cartridge
[0390] In some embodiments, the invention includes a cartridge for
coupling to the droplet microactuator. It will be appreciated that
a cartridge, while not necessary to the operation of the invention,
may be convenient in some circumstances. When present, the
cartridge may include a means for electrically coupling the path or
network of the droplet microactuator to a processor, e.g., a
processor of a droplet microactuator system of the invention. In
this embodiment, the electrical connection is:
electrodes--cartridge--processor, where there may be additional
elements between the three. In another embodiment, the cartridge
may include means for physically coupling to the droplet
microactuator. In this embodiment, the electrical connection may
be: electrodes--processor--cartridge. Alternatively, the cartridge
may lack electrical components altogether.
[0391] When present, the cartridge may include reservoirs for one
or more reagents, e.g., pre-loaded reagents. The droplet
microactuator may be configured so that a fluid path may be
established between the cartridge reservoirs and the interior of
the droplet microactuator for flowing reagents, sample and/or
filler fluid from the cartridge onto the droplet microactuator. For
example, preloaded cartridge reservoirs may be dispensed into the
droplet microactuator prior to, during, or after coupling of the
cartridge to the analyzer. The cartridge may be sealed,
self-contained and/or disposable. It may be supplied with or
without a droplet microactuator. Such cartridges can be used to
ensure repeatable assay conditions, permit safe handling and
disposal of infectious or hazardous material, and/or reduce
cross-contamination between runs. The cartridge may, for example,
include a machined plastic part. It may be affixed to and provided
in combination with the droplet microactuator.
[0392] The cartridge materials are selected to provide storage of
reagents without degradation or contamination of the reagents.
Moreover, they should be selected to provide reliable operation at
elevated temperature and to ensure compatibility with the real-time
chemistry. They may, for example, include molded plastic
components. In some embodiments, sealed, disposable test cartridges
enhance operator safety and facilitate safe disposal.
[0393] Various components of the droplet microactuator system may
be included on the cartridge. For example, present, the top-plate,
which encloses the interior space of the droplet microactuator, may
be provided as a component of the cartridge. Various sensors may
also be included as components of the cartridge.
8.8.3 Filler Fluid
[0394] The droplet microactuator of the invention includes one or
more free (i.e. fluid-fluid) interfaces. Examples include a
liquid-liquid or liquid-gas interface. Typically chemistry is
performed in the primary (droplet) phase, and the secondary phase
serves as a filler fluid separating the droplets from each other.
The secondary phase can, for example, be a liquid, gel and/or a
gas. Where the secondary phase includes a liquid, the liquid is
sufficiently immiscible with the primary liquid phase to permit the
droplet microactuator to conduct one of more droplet
operations.
[0395] It should also be noted that the droplet microactuator may
include more than two phases. For example, in one embodiment the
droplet microactuator operates based on an aqueous-oil-air
three-phase system. In a related environment, the droplet
microactuator may operate based on an aqueous-first oil-second oil
three-phase system, such as a system including an aqueous droplet
surrounded by silicon oil, which is in turn surrounded by a
fluorosilicon oil. Generally, three-phase systems will include
three components which are mutually immiscible or substantially
immiscible.
[0396] In another embodiment, oil or another immiscible liquid may
be used as a droplet encapsulant for electrowetting. For example, a
droplet can be encapsulated in a shell of oil by moving the droplet
through an air/oil interface. Each droplet would then have its own
local bath of oil with the space between encapsulated droplets
filled with either air or a third immiscible liquid. Among other
advantages, this approach is useful for minimizing the transfer of
material between droplets in the system by partitioning into the
oil phase while retaining the advantageous properties of the oil
with respect to evaporation and fouling of the surface. This
approach may also be used to facilitate electrowetting of
non-electrowettable liquids which are immiscible with
electrowettable liquids. In a specific embodiment of this concept
the immiscible liquid can be chosen to be crosslinkable (by UV,
heat, moisture or chemically) to create capsules of liquids with
solid shells, for drug delivery synthesis applications.
[0397] Further, in some applications it may be desirable or
necessary to perform certain operations in an immiscible liquid,
such as oil, and others in air. The invention includes hybrid
systems in which droplet manipulation is performed both in air and
in an immiscible liquid filler fluid such as oil. For example,
samples may be processed under oil and then transported into an
air-medium portion for evaporation for subsequent analysis by MS.
Conversely, a sample could be collected in air and then processed
with droplets under oil. Thus, the droplet microactuator may
include a transport path for moving droplets from a droplet
microactuator surface in a space filled with filler fluid to a
droplet microactuator open to the atmosphere or including a gaseous
filler fluid.
[0398] The filler fluid may be any fluid in which the droplet
microactuator can, under the right conditions, conduct one or more
droplet operations. It should be noted that certain filler fluids
may be solids or highly viscous fluids under certain conditions,
e.g., during transport, while they are transformed into fluids for
operation, e.g., by heating. The filler fluid may be a liquid or
gas during operation of the droplet microactuator. Examples of
suitable liquid filler fluids include, without limitation, silicone
oils; fluorosilicone oils; hydrocarbons, including for example,
alkanes, such as decane, undecane, dodecane, tridecane,
tetradecane, pentadecane, hexadecane; aliphatic and aromatic
alkanes such as dodecane, hexadecane, and cyclohexane, hydrocarbon
oils, mineral oils, paraffin oils; halogenated oils, such as
fluorocarbons and perfluorocarbons (e.g. 3M Fluorinert liquids);
mixtures of any of the foregoing oils in the same class; mixtures
of any of the foregoing oils in different classes. Examples of
suitable gas filler fluids include, without limitation, air, argon,
nitrogen, carbon dioxide, oxygen, humidified air, any inert gases.
In one embodiment, the primary phase is an aqueous solution, and
the secondary phase is air or an oil which is relatively immiscible
with water. In another embodiment, the filler fluid includes a gas
that fills the space between the plates surrounding the droplets. A
preferred filler fluid is low-viscosity oil, such as silicone oil.
Other suitable fluids are described in U.S. Patent Application No.
60/736,399, entitled "Filler Fluids for Droplet-Based
Microfluidics" filed on Nov. 14, 2005, the entire disclosure of
which is incorporated herein by reference. The fluid may be
selected to prevent any significant evaporation of the
droplets.
[0399] The phases of the fluids used in the protocols of the
invention may be selected to facilitate protocols of the invention
without undue formation of bubbles, loss of reagent to the filler
fluid, and/or adherence of reagent to the droplet microactuator
surface.
[0400] In certain embodiments of the invention the filler fluid may
be selected to reduce or prevent evaporation of sample, reagent, or
other droplets utilized in the protocols of the invention. The
filler fluid may be selected to prevent sample, reagent, or other
droplets utilized in the protocols of the invention from
evaporating and becoming too small for further effective
manipulation. Similarly, the filler fluid can be selected to
prevent evaporation of sample, reagent, or other droplets utilized
in the protocols of the invention from detrimentally concentrating
species within the droplets in a manner which results in an unduly
adverse affect on the intended use of the droplet. Moreover, the
filler fluid may be selected to reduce or prevent transport of
material from sample, reagent, or other droplets utilized in the
protocols of the invention across the phase boundary to maintain
droplet volume and/or ensure reliable microfluidic operation and/or
assay results. Miscibility between phases can sometimes result in
shrinking (or swelling) of the droplet phase. To prevent or reduce
this problem, one or more phases of the system may be saturated
with the equilibrium concentration of another phase to reduce
shrinking or swelling. Thus, for example, the filler fluid may be
saturated with the equilibrium concentration of the solvent for
sample, reagent, or other droplets utilized in the protocols of the
invention, and/or one or more of the sample, reagent, and/or other
droplets utilized in the protocols of the invention may be
saturated with the equilibrium concentration of the filler
fluid.
[0401] In some embodiments, a liquid filler fluid is selected to
minimize contact between the droplet and droplet microactuator
surfaces. That is, a film of liquid may exist between the droplet
and surface which prevents material within the droplet from coming
into contact with and adhering to the coated surface. This approach
helps to prevent fouling of the surface and related interference
with droplet transport. For example, it has been observed that high
concentrations of certain proteins in water droplets readily stick
to certain hydrophobic surfaces spoiling the hydrophobic nature of
these surfaces; whereas, the same droplets can be moved across the
same surfaces without appreciable adhesion of proteins if bathed in
an oil which minimizes contact between the two surfaces. This
approach may also help to avoid cross-contamination between
droplets caused by deposition of material from one droplet which is
then picked up by a second droplet. In a similar embodiment, a film
between the droplet and droplet microactuator surface can be used
to lubricate the droplet by preventing friction-like physical
interactions between the droplet and surface during droplet
operations.
[0402] In one embodiment, the invention provides a thin coating of
a liquid filler fluid layer in an otherwise gas filled system. For
example, the invention provides a microfluidic system including an
open or enclosed system including a thin layer of filler fluid,
such as oil, layered on a droplet microactuator surface, wherein
the system is otherwise filled with a gas. The oil is of sufficient
thickness to provide lubrication and contamination of droplet
microactuator surfaces and contamination of droplets via droplet
microactuator surfaces. Preferably the oil is selected to minimize
transport of material between the droplet and oil phases. One
advantage of this approach is reduction of carry-over in the
droplet microactuator. The surface may in some embodiments be
treated by coating it with the filler fluid while operating in air.
This approach is also useful for loading operations as a means to
retain the lubricating effect of oil while avoiding trapping of oil
bubbles in the bulk filler fluid.
[0403] Treatment of a Teflon AF surface with silicone oil can
provide some of the lubrication benefit of silicone oil filler
fluid even when operating in air. This approach can be used to
prime the droplet microactuator with a lubricating layer of oil,
followed by replacement with air to allow samples to be loaded
without introduction of bubbles, followed by re-introduction of oil
to prevent evaporation of the samples. Thus the benefits of each
kind of system are available depending on the type of microfluidic
processing to be carried out.
[0404] In another embodiment, the filler fluid can be completely
exchanged at different steps within a protocol. For example, a gas
filler fluid can be introduced during sample loading to prevent
trapping of air bubbles and then a liquid filler fluid can be
pumped in to prevent evaporation of the liquid. Different types of
filler fluid can be pumped into or out of the system depending on
the particular assay steps to be performed.
[0405] In yet another embodiment, multiple filler fluids can be
used within a single system. For example, a droplet microactuator
can be selected to have separate gas filled and liquid filled
regions. Operations or certain types of droplets can be segregated
between the different filler fluid regions.
[0406] The filler fluid may be selected based on its refractive
index to either match the droplet to prevent refraction of light
passing through or near the droplet. Alternatively the filler fluid
may be selected with a refractive index that differs from the
droplet to provide contrast for certain types of optical
measurements or optical manipulations. A filler fluid may be chosen
to have a lower index of refraction than the primary liquid so that
light can be transmitted though the primary liquid by total
internal reflection. The primary phase can include highly elongated
droplets which can serve as "light pipes" to convey light between
two locations, e.g. to facilitate optical analyses.
[0407] The filler fluid may be selected based on its color to
facilitates direct or indirect visualization of the droplet, e.g.,
by providing contrast between the sample, reagent, and/or other
droplets used in the protocols of the invention and the filler
fluid. This approach can enhance visualization of the different
phases, for example to distinguish droplets from filler fluid or
from air bubbles. In optical applications, the differential
absorbance of the two phases can be used to modulate the color of
light passing through the system. As another example, in
applications where fluorescence measurements are made within
droplets it may desirable for the oil to include molecules, such as
dyes, that absorb the emitted wavelength of light to minimize
cross-talk between reactions occurring in adjacent droplets.
[0408] The filler fluid may be selected to have particular thermal
properties that can either thermally insulate the droplets or
conduct heat away from the droplets. For example, in the
amplification protocols of the invention, a thermally conductive or
low heat capacity filler fluid may be desirable to permit rapid
changes in temperature. For applications where a steady temperature
is required a thermally insulating or high heat capacity filler
fluid can be used to provide temperature stability.
[0409] The filler fluid may be selected to undergo a phase change
upon presentation of an appropriate stimulus. For example, a
wax-like filler fluid (e.g. paraffin wax or octadecane) can be used
where the filler fluid is changed from solid to liquid form by
application of heat. Lowering the temperature would return the
filler fluid to a solid so that droplets would be contained within
a solid matrix. Encapsulation of the liquid phase within a solid
may facilitate storage and handling of the sample, reagent, and/or
other droplets utilized in the protocols of the invention and/or
allow for safe and convenient disposal of the materials following
use of the droplet microactuator. The filler fluid can be stored as
a solid on the droplet microactuator, in a cartridge-based
reservoir, or elsewhere, and heated to permit the fluid to flow
into and fill the droplet microactuator. Or the immiscible filler
fluid can be selected to be crosslinkable (by UV, heat, moisture or
chemically) to create capsules of liquids within a solid shell.
[0410] The filler fluid may be selected to have particular gas
permeability or saturation properties. In certain applications a
reaction occurring inside the droplet may consume oxygen or other
gas which may need to be replenished by gas contained within or
transported through the filler fluid. For example, some fluorinated
oils have useful gas permeability properties for such applications.
Alternatively, the filler fluid may be selected to exclude certain
gases from the droplet, for example to maintain anaerobic
conditions within the droplet. The filler fluid may be selected to
have a certain degree of miscibility or partitioning into the
droplet phase. Usually, complete or substantially complete lack of
miscibility between the droplet and filler fluid is desired, but
some applications may benefit from some limited degree of
miscibility between the phases or partitioning of particular
molecules between the phases, e.g., liquid-liquid extraction
applications. In certain applications where dissolved gases in the
filler fluid may be problematic, a means for degassing the filler
fluid prior to or during use may need to be provided. For example,
filler fluid may be degassed by incubation under vacuum, heating,
sparging or by centrifugation.
[0411] The filler fluid may be selected to have a particular
surface or interfacial tension with the droplet phase or with the
droplet microactuator surfaces. Surfactants can be added to the
filler fluid to stabilize liquid films that may be present between
the droplet and solid phases. Examples of suitable surfactants
include nonionic low HLB (hydrophile-lipophile balanced)
surfactant. The HLB preferably less than about 10 or less than
about 5. Suitable examples include: Triton X-15 (HLB=4.9); Span 85
(HLB 1.8); Span 65 (2.1); Span 83 (3.7); Span 80 (4.3); Span 60
(4.7); and fluorinated surfactants.
[0412] Surfactants are preferably selected and provided in an
amount which (1) results in more droplet operations on the droplet
microactuator as compared to corresponding droplet microactuator
without the surfactant; or (2) makes one or more droplet operations
possible on the droplet microactuator as compared to corresponding
droplet microactuator without the surfactant; or (3) makes one or
more droplet operations more reliable on the droplet microactuator
as compared to corresponding droplet microactuator without the
surfactant. In a related example, surfactants are preferably
selected and provided in an amount which makes one or more droplet
operations possible or more reliable for droplets including one or
more specific reagents or mixtures on the droplet microactuator as
compared to droplet operations for the same droplets including one
or more specific reagents or mixtures on a corresponding droplet
microactuator without the surfactant. In another related example,
surfactants are preferably selected and provided in an amount which
makes one or more droplet operations possible or more reliable for
one or more droplets including amphiphilic molecules on the droplet
microactuator as compared to droplet operations for the same
droplets including amphiphilic molecules on a corresponding droplet
microactuator without the surfactant.
[0413] In a preferred embodiment, the surfactant is added to the
filler fluid in an amount which ranges from about 0.001 to about
10% w/w, or about 0.001 to about 1% w/w, or about 0.001 to about
0.1% w/w. For example, in one embodiment the filler fluid is 2 cSt
silicone oil and the surfactant is Triton X-15 in an amount which
ranges from about 0.001 to about 10% w/w, or about 0.001 to about
1% w/w, or about 0.001 to about 0.1% w/w. The solid-liquid
interfacial tension may be adjusted to control the wetting of the
filler fluid on the droplet microactuator surfaces, for example, to
control the formation, thickness or behavior of thin films of the
filler fluid between the droplet and droplet microactuator surfaces
or to control the wetting behavior of the fluid when filling or
emptying it from the droplet microactuator.
[0414] By doping filler fluid with surfactant, the inventors have
discovered that it is possible to increase the concentrations of
compatible protein solutions by more than 3 orders of magnitude,
from mg/L to mg/mL. The inventors were able to reliably dispense
and transport 25 mL droplets of 75 mg/mL lysozyme solution using
the new filler fluid. For example, the filler fluid may be a
silicone oil doped with a surfactant, such as Triton X-15.
Preferably the surfactant is a lipophilic surfactant. In one
embodiment, we added 0.1% (w/w) Triton X-15, a lipophilic
surfactant, to the oil so that high concentrations protein droplets
could be formed or dispensed from on-chip reservoirs. Droplet
transport for all compatible fluids is fast (typically about 3-10
cm/sec) and reliable (>25,000 operations). In one embodiment,
the filler fluid includes a surfactant dopant in an amount which
results in an increase in the concentration of a protein that can
be reliably dispensed on the droplet microactuator.
[0415] The filler fluid may be selected to have a particular
viscosity or volatility. For example, a low viscosity liquid (e.g.
0.65 cSt. Silicone oil) facilitates transport of droplets while a
low volatility filler fluid (e.g., 2, 5 or 10 cSt. Silicone oil)
may be desirable to prevent loss of filler fluid by evaporation,
particularly in nucleic acid amplification applications performed
at elevated temperature. In some applications, evaporation of the
filler fluid can be desired, so a low volatility filter fluid may
be selected. The filler fluid may be selected to have a particular
viscosity dependence on temperature, since the viscosity of the
filler fluid affects the fluid dynamics and the temperature on the
droplet microactuator may vary. In nucleic acid amplification
protocols of the invention, the filler fluid is selected so that
any viscosity changes resulting from thermal cycling are not unduly
detrimental to conducting droplet operations required for effecting
the amplification protocols.
[0416] The filler fluid may be selected to have particular
electrical properties. For example, certain applications including
electrowetting favor the use of a filler fluid that is
non-conductive (e.g., silicone oil). Or the dielectric permittivity
can be selected to control the coupling of electrical energy into
the system from external electrodes. In certain applications a
non-conductive filler fluid can be employed as an electrical
insulator or dielectric in which the droplet floats just above the
electrodes without physically contacting them. For example, in an
electrowetting system a layer of filler fluid (e.g., silicone oil)
between the droplet and electrode can be used to provide
electrostatic control of the droplet. Filler fluids may be
deionized to reduce conductivity.
[0417] The filler fluid may be selected to have a particular
density relative to the droplet phase. A difference in density
between the two phases can be used to control or exploit buoyancy
forces acting upon the droplets. Examples of two-phase systems
useful in this aspect of the invention include water/silicone oil,
water/flourinert, and water/fluorosilicone oil. When one phase is
buoyant, then that effect can be exploited in a vertical
configuration as a means to transport one phase through the other.
For example, a waste or collection well can exist at the top or
bottom of the droplet microactuator where droplets are delivered to
that reservoir by simply releasing them at an appropriate point and
allowing them to float or sink to the target destination. Such an
approach may be suitable for use in removing reactant from a
droplet microactuator, e.g. removing fluid containing amplified
nucleic acid for use in other processes. Density differences can
also be used as a means to control or engineer contact between the
droplets and droplet microactuator surfaces. For example, a droplet
not normally contacting a top-plate can be released to sink or
float to that surface to contact it. Density differences and
buoyancy effects can also be exploited for sensing applications in
which the movement of droplets is detected and related to a change
in position, orientation or acceleration.
[0418] The filler fluid is selected for material compatibility with
the droplet microactuator surfaces. For example, certain filler
fluids can etch, dissolve, contaminate, absorb into or otherwise be
incompatible with certain droplet microactuator materials. For
example, fluorinated hydrocarbons, such as Fluorinert, may be
incompatible with Teflon AF or Cytop surfaces because of their
tendency to dissolve these materials, while silicone oils may be
incompatible with PDMS surfaces due to the tendency of these
materials to dissolve each other.
[0419] The filler fluid is selected for biochemical compatibility
with sample and reagents used in the protocols of the
invention.
[0420] The invention may include means for controlling the
introduction or circulation of the filler fluid within the droplet
microactuator, cartridge and/or system. In one mode of operation
the filler fluid is injected once during the initialization of
droplet microactuator operation. The filler fluid may be provided
from an external source using a syringe, dropper, pipettor,
capillary, tube or other means. Alternatively, the filler fluid may
be provided from a reservoir internal to the droplet microactuator
assembly or cartridge. As an example, the fluid can be contained
within a sealed pouch which is punctured or compressed to transfer
the liquid into the droplet microactuator.
[0421] In another mode of operation a means can be provided for
multiple introductions or recirculation of one or more filler
fluids within the droplet microactuator. A secondary fluid-handling
system can be provided to inject and to remove fluid from within
the droplet microactuator. Pressure, gravity or other means such as
the use of thermal gradients can be used to transport the filler
fluid into or out of the droplet microactuator. Such a system can
be used for the following purposes: [0422] (1) To replenish filler
fluid lost to evaporation or leakage over time. A slow steady flow
or periodic injection of filler fluid can be employed to make up
for any loss of filler fluid volume. [0423] (2) To provide "clean"
filler fluid either continually or periodically to reduce
contamination between droplets. The filler fluid can be cleaned
either by completely replacing it or by circulating it through a
filter or bed of absorbent material selected to remove
contaminants. [0424] (3) To provide a means for transporting
droplets to waste. For example, at the end of an assay, droplets
can be released and allowed to flow with the filler fluid to the
outlet providing a means to "flush" the droplet microactuator.
Flushing the droplet microactuator can be performed to reset the
status of the droplet microactuator in preparation to perform
additional assays. [0425] (4) To exchange the filler fluid when
different fluids may be desired for certain steps, for example to
replace oil with air to allow drying of droplets, or to replace one
oil with a different oil. [0426] (5) To provide a means of
controlling the temperature of the droplets by heating or cooling
the fluid as it is circulated through the droplet microactuator.
For example, PCR can be performed in droplets containing the
appropriate PCR reagents (e.g., primers, nucleotides, and
polymerase) by circulating temperature controlled filler fluid
through the droplet microactuator to perform thermocycling. The
temperature of the filler fluid entering and leaving the droplet
microactuator can be directly measured and the temperature and flow
rate of the filler fluid can be adjusted to provide optimal
temperature control inside the droplet microactuator.
[0427] Local regions of filler fluid or even individual units of
filler fluid for each droplet can be used. For example aqueous
droplets can be encapsulated in an individual shell of fluid, such
as oil, which moves along with that droplet. Each such droplet
would then have its own local fluid bath with the space between
encapsulated droplets filled with third immiscible liquid such as
air or fluorosilicone oil. This approach can be used to minimize
the transfer of material between droplets in the system by
partitioning into the oil phase while retaining the advantageous
properties of the oil with respect to evaporation and fouling of
the surface. The shells of oil can be created by simply moving the
droplet through an oil interface, pinching off a unit of oil as the
droplet creates a bulge along the interface.
[0428] Hybrid systems can be implemented in which different regions
of the droplet microactuator are filled with different fluids. For
example, samples can be processed under oil and then transported
into an air portion to be evaporated for subsequent analysis by MS.
Conversely, a sample can be collected in air and then processed
under oil.
[0429] Magnetically responsive beads can be used to move material
between oil and water phases on a droplet microactuator. Generally,
water-soluble compounds or materials tend to remain within the
droplets, unable to cross the oil-water meniscus in significant
quantities, and oil-soluble compounds or materials remain in the
lipophilic filler fluid. When the material is attached to
magnetically responsive beads, a magnetic field may be used to move
the beads and attached material across the oil-water boundary. The
beads need to be selected such that they have sufficient affinity
for oil and water so that they can readily cross the meniscus. This
operation is useful for drying or concentrating materials and can
also be used to facilitate washing and/or dilution. For example,
material bound to a magnetically responsive bead can be removed
from one droplet and transferred by way of the filler fluid to
another droplet.
[0430] Filler fluid can be circulated through the droplet
microactuator to reduce contamination during and/or between runs.
Filler fluid can be continually or periodically flowed through the
droplet microactuator, so that fresh filler fluid is constantly
supplied to the droplet microactuator. In addition to removing
contaminates contaminated oil, this technique could be used at the
end of a run to clear droplets from the array by removing the
voltage so that droplets are released and flow with the oil to an
exterior of the droplet microactuator and/or into a waste
reservoir.
8.8.4 Droplet Microactuator Loading
[0431] The droplet microactuator generally includes one or more
input ports for the introduction of one or more filler fluids,
reagents and/or samples (e.g., reagents and/or samples for
conducting protocols and/or assays as described elsewhere herein,
e.g., in Sections 8.1, 8.2, 8.3, 8.4 and/or 8.5) into the droplet
microactuator. In some embodiments, samples or reagents are loaded
via the input ports using conventional robotics. In one alternative
embodiment, droplets of sample or reagent are separated by plugs of
oil in a long pre-loaded glass capillary which when connected to
the droplet microactuator allows droplets of sample or reagent to
be captured and routed on the droplet microactuator as they are
pumped out of the capillary into the input port. Another loading
technique involves pre-stamping reagents onto the droplet
microactuator and allowing them to dry, e.g., using a high-speed
reagent stamping or printing process. Yet another approach involves
the use of a direct plate-to-droplet microactuator interface in
which the contents of plates, e.g., 1536 or 384 or 96 well plates,
are transported onto the droplet microactuator in parallel by using
pressure to force the contents through input ports aligned with
wells. Loading hardware may in some embodiments be electronically
coupled to and controlled by the controller.
8.8.5 Reservoirs
[0432] The droplet microactuator includes various reservoirs, such
as input reservoirs and/or processing reservoirs.
8.8.5.1 Input Reservoirs
[0433] In some embodiments, the droplet microactuator includes one
or more input reservoirs in fluid communication with one or more
input ports, typically in direct fluid communication with the input
ports. The input reservoir(s) serve as reservoirs for storage of
bulk source material (e.g. reagents or samples) for dispensing
droplets (e.g. reagent droplets or sample droplets). Thus, the
input reservoir(s) may, for example, serve as sample wells or
reagent wells.
[0434] The input reservoirs generally include one or more well
walls defining an interior space and an opening. The interior space
defined by the well walls is at least partially isolated by the
well walls from the remainder of the interior of the droplet
microactuator. The well may be adjacent (in any direction, e.g.,
vertically or laterally) to a port suitable for introduction of
fluid from an exterior of the droplet microactuator into the input
reservoir. One or more openings in the well walls may be provided
to enable fluid communication with the interior volume of the
droplet microactuator for dispensing of droplets into this interior
volume. The opening(s) may permit fluid to flow or be transported
into the interior volume of the droplet microactuator onto the path
or network of electrodes. Input reservoirs may also include one or
more vents for permitting displacement of filler fluid from the
input reservoir as fluid is introduced into or removed from the
well via the port or the opening.
[0435] The input reservoirs may further include one or more planar
control electrodes in a top or bottom plate adjacent to or within
the space defined by the well walls. The planar electrodes are
electronically coupled to and controlled by the controller. In a
preferred embodiment, the planar electrode has two or more branches
or rays, such that activation of the control electrode during
droplet dispensing in the presence of a fluid exerts a "pull" on
the fluid in a direction which is generally opposite to the
direction of droplet dispensing. In some cases, the shape of the
electrode results in a multi-vector pull having a mean vector which
has a direction generally opposite to the direction of the droplet
being dispensed.
[0436] Well walls may, for example, be formed by protrusions from
the top or bottom plates, and/or may be formed by deposition of a
wall-forming material on a surface of the top or bottom plate. For
example, well walls may be formed from a soldermask material or
polymeric gasket material deposited and patterned on the surface.
In some embodiments a source of continuous or semi-continuous
sample or reagent flow is coupled in fluid communication with one
or more of the input ports.
[0437] It should be noted that while droplet dispensing may be
conducted from defined reservoirs, in some embodiments, droplet
dispensing is conducted without the use of physically defined
reservoirs. Dispensing may proceed from source droplet which is
confined during droplet dispensing, e.g., by electrowetting forces
or by hydrophilic surfaces.
8.8.5.2 Processing Reservoirs
[0438] The droplet microactuator may also include one or more
processing areas or reservoirs. These areas or reservoirs serve as
a location for executing various droplet processing steps, such as
mixing, heating, incubating, cooling, diluting, titrating, and the
like. The droplet microactuator includes one or more paths or
networks of control electrodes sufficient to transport droplets
from the one or more input ports to the one or more processing
areas or reservoirs. In some cases the processing areas are simply
components or sections of these paths or networks. In other
embodiments, the processing areas are defined processing
reservoirs. Such reservoirs may, for example, be structured
generally in the same manner as the input reservoirs described
above. However, the processing reservoirs are typically not in
direct fluid communication with the input ports, i.e., droplet
transport along the one or more paths or networks of control
electrodes is required add reagent or sample to the processing
reservoir(s). In some cases, the processing reservoirs include a
path or network of reservoirs therein to permit droplet operations
within the processing reservoirs.
8.8.5.3 Droplet Operations
[0439] The droplet microactuator may conduct various droplet
operations with respect to a droplet. Examples include: loading a
droplet into the droplet microactuator; dispensing one or more
droplets from a source droplet; splitting, separating or dividing a
droplet into two or more droplets; transporting a droplet from one
location to another in any direction; merging or combining two or
more droplets into a single droplet; diluting a droplet; mixing a
droplet; agitating a droplet; deforming a droplet; retaining a
droplet in position; incubating a droplet; heating a droplet;
vaporizing a droplet; cooling a droplet; disposing of a droplet;
transporting a droplet out of a droplet microactuator; other
droplet operations described herein; and/or any combination of the
foregoing.
[0440] Droplet dispensing refers to the process of aliquoting a
larger volume of fluid into smaller droplets. Dispensing is
usefully employed at the fluidic interface, the input reservoirs,
and at processing reservoirs. Droplets may be formed by energizing
electrodes adjacent to the fluid reservoir causing a "finger" of
fluid to be extended from the reservoir. When the fluid front
reaches the terminal electrode, the intermediate electrodes are
de-energized causing the fluid to retract into the reservoir while
leaving a newly-formed droplet on the terminal electrode.
[0441] As previously noted, one or more electrodes in the reservoir
may also be energized to assist in separating the droplet being
dispensed from the bulk fluid. Because the droplet conforms to the
shape of the electrode, which is fixed, excellent accuracy and
precision are obtained. Droplet dispensing is controlled by the
controller. In some embodiments the invention employs droplet
dispensing structures and/or techniques described in U.S. Pat. No.
6,911,132, entitled "Apparatus for Manipulating Droplets by
Electrowetting-Based Techniques," issued on Jun. 28, 2005 to Pamula
et al.; U.S. patent application Ser. No. 11/343,284, entitled
"Apparatuses and Methods for Manipulating Droplets on a Printed
Circuit Board," filed on filed on Jan. 30, 2006; U.S. Pat. Nos.
6,773,566, entitled "Electrostatic Actuators for Microfluidics and
Methods for Using Same," issued on Aug. 10, 2004 and 6,565,727,
entitled "Actuators for Microfluidics Without Moving Parts," issued
on Jan. 24, 2000, both to Shenderov et al., the disclosures of
which are incorporated herein by reference.
[0442] In some embodiments, droplet operations are mediated by
electrowetting techniques. In other embodiments, droplet operations
are mediated by electrophoresis techniques. In still other
embodiments, droplet operations are mediated by electrowetting
techniques and by electrophoresis techniques.
[0443] In one embodiment, separations may be performed using a
combination of electrowetting and electrophoresis. Electrowetting
microactuation can be used to create a channel to perform
electrophoresis; to deliver a sample to the channel or capture a
sample fraction from channel following an electrophoretic
separation. For example, for forming a channel, electrowetting can
be used to deform (stretch) a droplet of separation medium in a
long thin shape followed. In some cases, the channel may be
polymerized, e.g., using UV polymerization. In other cases, the
channel may be formed by using droplet operations to add droplets
into a physically confined microchannel. In a related embodiment,
the effective length of an electrophoresis channel can be increased
by capturing the fraction of interest in a droplet at the output
and then returning it to the input in a cyclical fashion. Using the
same principle, a series of progressively finer separation can be
performed. Separations may also be accomplished using multiple
different separation mediums at the same time.
[0444] Droplet splitting or dividing of droplets generally involves
separating a droplet into two or more sub-droplets. In some cases,
the resulting droplets are relatively equal in size.
[0445] Transporting involves moving a droplet from one location to
another in any direction. Droplets may be transported on a plane or
in three dimensions. It will be appreciated that a variety of
droplet operations, such as dispensing and/or splitting may include
a transporting element, in which on droplet is transported away
from another droplet.
[0446] Merging involves combining two or more droplets into a
single droplet. In some cases, droplets of relatively equal size
are merged into each other. In other cases, a droplet may be merged
into a larger droplet, e.g., combining droplet with a larger volume
present in a reservoir.
[0447] Mixing a droplet involves various droplet manipulations,
such as transporting or agitating, that result in a more homogenous
distribution of components within the droplet. In one mixing
embodiment, a droplet positioned over an electrowetting electrode
is rapidly and cyclically deformed in place by activating and
deactivating the electrode, inducing fluid currents within the
droplet which facilitate mixing. Frequency-dependent effects such
as mechanical resonances may be used to tune the quality and speed
of mixing. Compared to techniques which require transport of
droplets on a surface for mixing this approach minimizes the area
required for mixing. This mixing scheme can be employed without the
presence of a top plate. Due to space-saving advantage, this scheme
could provide for simplified mixing in reaction wells since only
one electrode is needed.
[0448] Reagents or samples from reservoirs may be dispensed as
discrete droplets for transport to other locations on the droplet
microactuator.
[0449] The invention includes droplet operations using droplets
comprising beads. A variety of such operations are described
elsewhere herein. In one embodiment, beads are used to conduct
droplet operations on reagents that are prone to interfere with
droplet operations. For example, certain proteins may be prone to
bind to surfaces of a droplet microactuator and/or to partition
into the filler fluid. Immobilizing such compounds on hydrophilic
beads can be used to facilitate droplet operations using the
compounds. The compounds can be bound to the beads, and the beads
can contained with a droplet which is subjected to droplet
operations.
[0450] In one particular dispensing operation, coagulation is used
to separate serum from whole blood. Whole blood is loaded onto the
chip and combined with a droplet comprising a coagulating agent.
Following coagulation, droplets are dispensed from the sample.
Because cells and platelets are trapped in place, the liquid
dispensed from the sample will contain only serum.
8.8.6 Thermal Control
[0451] The droplet microactuator of the invention may include a
means for controlling the temperature of the droplet microactuator
or a region of the droplet microactuator. Among other things,
thermal control is useful for various protocols requiring heating
or cooling steps. Examples include amplification protocols
requiring thermal cycling and various assays that require
incubation steps.
8.8.6.1 Thermal Control Designs
[0452] In general, thermal control may be provided in three ways:
(1) thermal control of the entire droplet microactuator; (2)
thermal control of a region of a droplet microactuator using a
heater that is in contact with or in proximity to the controlled
region; and (3) thermal control of a region of the droplet
microactuator using a heater that is integrated into the droplet
microactuator (e.g., in the substrate comprising the path or array
of electrodes and/or in a top plate of the droplet microactuator,
when present). Combinations of the foregoing approaches are also
possible. Two approaches previously discussed are illustrated in
FIG. 2.
[0453] In an integrated heater approach, temperature zones can be
created and controlled using thermal control systems directly
integrated into the droplet microactuator. Integration of thermal
control through thin-film heating elements fabricated directly on
the droplet microactuator is also useful to maximize the speed,
throughput and quality of amplification reactions on the droplet
microactuator. Due to their small thermal mass, droplets can be
thermally cycled extremely rapidly. Thermal control is enhanced by
locating the heating elements proximate to the droplets and
reducing the parasitic thermal losses between the heater and the
droplet. Heating elements can be integrated into the top plate
and/or bottom plate of the droplet microactuator.
[0454] Integrating heating elements onto the droplet microactuator
also enables the use of multiple distinct thermal zones within the
droplet microactuator. This permits multiple steps in an analysis,
such as sample preparation and thermal cycling, requiring different
temperatures to be performed simultaneously on different portions
of the droplet microactuator. Droplets can be physically
transported or "shuttled" between zones of different fixed
temperatures to perform the thermal cycling aspects of the
amplification reaction. This approach can produce even faster
reactions, since heating and cooling of the entire thermal zones is
no longer rate-limiting. Instead, heating and cooling rates are
determined by the time required to transport the droplets between
the zones and the time required for the droplet temperature to
equilibrate to the temperature of the zone once it arrives within
the zone, both of which are expected to be very fast. A further
advantage is that reaction steps can be "queued" rather than
"batched" to permit greater operational flexibility. For example,
discrete samples can be continuously fed into the droplet
microactuator rather being delivered at a single point in time.
[0455] Droplets may be thermally cycled in batch mode using a
single heater or in flow-through mode by circulating the droplets
through distinct temperatures zones created by the heating
elements. The essential difference between batch and flow-through
modes is that in batch mode thermal control is effected by varying
the temperature of the heater while in flow-through mode, thermal
cycling is effected by transporting the droplets among distinct
constant temperature zones. In the "batch" method a single
integrated thin-film heater on the droplet microactuator was used
to thermally cycle static droplets located within the heater zone.
In the "flow-through" method, two distinct fixed temperature zones
were created on the droplet microactuator and thermal cycling was
performed by shuttling the droplets between the two zones.
[0456] In the "batch" case, the thermal mass of the heater itself
as well as thermal losses may be minimized through the use of
thin-film heaters placed directly adjacent to the droplets. Because
the thermal masses, including the droplet itself, are so small,
rapid temperature changes can be effected. Passive cooling (in
filler fluid) is also rapid because the total energy input into the
system is extremely small compared to the total thermal mass.
[0457] For "flow-through" heating, a larger thermal mass is
desirable because it helps to stabilize the temperature while a
slower ramp rate is tolerable because the heater temperature is not
varied once it reaches its set point. A flow-through system can,
for example, be implemented using block heaters external to the
droplet microactuator which were more accurate and easier to
control than thin-film heaters although, in principle either type
of heater could be used to implement either method.
[0458] In another embodiment, temperature is controlled by flowing
or recirculating heated filler fluid through the chip and around
the droplets.
[0459] The droplet microactuator layout is scalable, such that a
droplet microactuator may include a few as one heating zone up to
tens, hundreds or more heating zones.
8.8.6.2 Heater Types
[0460] Heaters may be formed using thin conductive films. Examples
of suitable thin films include Pt heater wires and transparent
indium-tin-oxide (ITO). ITO provides better visualization of the
droplets for real-time observation. A remotely placed conventional
thermocouple (TC) for temperature regulation can also be used. In
one embodiment, tiny metal (e.g., copper) vias in the PCB substrate
are used to create tight thermal junctions between the liquid and
the remote TC. Further, sample temperature can be determined by
monitoring the copper via using a surface mount thermistor or an
infrared sensor. One advantage of using a thermistor is that they
are small enough (2.times.2 mm) to be soldered directly on the
droplet microactuator, while an advantage of using IR is that it is
non-contact method which would simplify the interfacing. Because
the thermal conductivity of copper is at least 700 times greater
than the FR4 substrate (350-390 W/m-K versus 0.3-0.5 W/m-K) the
temperature of a Cu via will accurately represent the temperature
inside the liquid. Heaters may be integrated on the bottom and/or
top (when present) plate of the droplet microactuator and on the
bottom and/or top surface of either plate, or integrated within the
structure of either plate.
[0461] In one flow-through embodiment, reduced thermal gradients
can be provided by using heaters to create a continuous temperature
gradient across the droplet microactuator (e.g., from 100 to
50.degree. C.). The use of a continuous gradient will eliminate the
need to overcome the steep temperature gradients found along the
edge of the heater blocks. A controlled temperature gradient would
also significantly enhance the functionality of the device by
allowing protocols with arbitrary numbers of temperature points to
be implemented. Furthermore, each reaction can be performed with a
custom thermal protocol while only the temperatures of the two or
more blocks would need to be thermally regulated. The droplets will
be transported to and held at the appropriate location between the
heaters to achieve a target temperature. The fluorescence of the
droplets can be imaged using a fluorescence sensor as they are
transported over a detection spot. The temperature of the upper and
lower target temperatures can be varied by changing the location of
the droplets.
[0462] In some embodiments, heaters located above the droplets may
obscure the droplets thus interfering with real-time optical
measurements. In such cases, the droplets can be transported out
from underneath the heaters to a location which is preferred for
optical detection (i.e. a detection spot). Droplets may be
periodically transported out from underneath the heaters to a
detection spot on the droplet microactuator detection purposes,
e.g. detection by fluorescence quantitation. Droplets may be routed
into proximity with a sensor while cycling them from one
temperature zone to another.
8.8.7 Droplet Microactuator Fabrication
[0463] Droplet microactuators can be made using standard
microfabrication techniques commonly used to create conductive
interconnect structures on microdroplet microactuators and/or using
printed-circuit board (PCB) manufacturing technology. Suitable PCB
techniques include those described in U.S. patent application Ser.
No. 11/343,284, entitled "Apparatuses and Methods for Manipulating
Droplets on a Printed Circuit Board," filed on Jan. 30, 2006, the
entire disclosure of which is incorporated herein by reference.
These techniques permit the droplet microactuator to be
manufactured in bulk at very low cost. Low cost manufacture enables
economical production of droplet microactuators, even for use as
one-use disposables. Thus, the invention provides a method in which
droplet microactuators are supplied to users as components of
disposable cartridges for use in systems of the invention.
[0464] Designs can also be implemented on glass or silicon using
conventional microlithography techniques with the capability of
producing much smaller features than are typical in a PCB process.
Even, for example, for a 1,572,864-reservoir droplet microactuator
with 70 .mu.m reservoir spacing and 3 fL reservoir volume, the
minimum required lithographic feature size is .about.0.5 .mu.m
which is well within the capabilities of conventional
microlithographic techniques currently used in the semiconductor
industry.
8.9 Systems
[0465] Fluid loading may be accomplished using droplet
microactuator systems, such as illustrated in FIG. 18. Steps of a
fluid loading protocol may be conducted using a droplet control
system 1801. A set of computer executable instructions may be
written which can be loaded into a controller for execution of a
loading protocol. Integrated systems including the droplet control
system 1801 and the protocol execution system 1802 may also be
used. The droplet control system 1801 permits a user to control
droplet microactuator system functions, such as droplet operations
and sensor operations for fluid loading protocols. The protocol
execution system 1802 permits a user to execute software routines
that control droplet microactuator system functions, such as
droplet operations and fluid loading operations. The invention also
provides a method or computer useable instructions for conducting
fluid loading processes or protocols. The programmable flexibility
of the platform permits assays to be rapidly optimized and allows
conditional execution steps to be implemented. For example,
calibrations, confirmatory tests, or additional controls can be
executed if triggered by a particular test result. In some
embodiments, the system can integrate sample preparation steps.
Automation of the system and on-droplet microactuator operations
enhance portability and enable assays to be performed more quickly
and by personnel with minimal training, thereby reducing human
error.
[0466] Referring further to FIG. 18, at a high level, each of the
systems of the invention typically includes a processor or
controller 1803, a droplet microactuator 1804, a sensor or detector
1805, input device(s) 1806, output device(s) 1807, and software.
U.S. Patent Application No. 60/806,412, entitled "Systems and
Methods for Droplet Microactuator Operations," filed on Jun. 30,
2006, the entire disclosure of which is incorporated herein by
reference, describes droplet microactuator systems which may be
employed in conjunction with the droplet microactuator aspects of
the invention. The droplet control system includes droplet control
software run on a computer 1808 and programmed to display a droplet
control interface for controlling droplet microactuator system
functions. The protocol execution system includes protocol
execution software programmed to facilitate execution of a set of
computer executable or computer useable instructions for
controlling droplet microactuator system functions to conduct fluid
loading.
8.9.1 Controller
[0467] The system of the invention may include a controller 1803.
The controller serves to provide processing capabilities, such as
storing, interpreting, and or executing software instructions. The
controller may, for example, be comprised of a digital signal
processor (DSP) with memory, a microcontroller or an application
specific integrated circuit (ASIC). An example of a suitable DSP
processor is the Analog Devices Blackfin DSP processor.
[0468] The controller is electronically coupled to various hardware
components of the invention, such as the droplet microactuator, any
sensors, and any input and/or output devices. The controller may be
configured and programmed to control data and/or power aspects of
these devices. For example, with respect to the droplet
microactuator, the controller controls droplet manipulation by
activating/deactivating electrodes. This aspect of the invention is
discussed further in Section 8.8.
[0469] The controller may further be electronically coupled to a
separate computer system including a processor, input and output
devices, data storage medium, and other components. This
arrangement is particularly useful in the droplet control system,
in which the computer system is programmed to operate a droplet
control user interface. In this arrangement, the processor of the
computer system may accept input via the user interface and
transmit instructions to the controller, e.g., to
activate/deactivate electrodes, to read electrodes, memory, and/or
sensors, and the like.
[0470] In the protocol execution system, software for controlling
the system may be loaded directly into and executed by the
controller to cause the controller to control the droplet
microactuator system functions. In this embodiment, the system can
run autonomously, e.g., as a portable or handheld system.
8.9.2 Droplet Microactuator
[0471] The system may include a droplet microactuator 1804, as
described further in Section 8.8. The droplet microactuator is
electronically coupled to the processor such that the processor can
control various operations of the droplet microactuator, such as
droplet manipulation operations.
8.9.3 Sensor
[0472] Various embodiments of the invention make use of sensors or
detectors 1805. Sensors may include sensors which are coupled to
the droplet microactuator for the purpose of measuring parameters
of interest on the droplet microactuator such as the fluorescent or
luminescent intensity at a location on the droplet microactuator
where a reaction product may be located. Sensors may also include
sensors which monitor the status of the system such as droplet
microactuator insertion sensors, lid latch sensors, ambient
temperature sensors and the like. Output from each sensor may be
mapped to a specific memory location, and the processor must only
query the mapped location to obtain a reading from the sensor. The
sensor is mounted relative to the droplet microactuator and/or
electronically coupled to the droplet microactuator such that the
sensor can detect signals, such as electrical or light signals,
from the droplet microactuator. Sensors are discussed in more
detail elsewhere in this specification, e.g., see Section 8.11.
8.9.4 Input and Output Device(s)
[0473] Systems of the invention also include various input devices
1806 and output devices 1807. In certain embodiments, such as the
protocol execution system, certain input and output devices may be
controlled using a human-machine interface (HMI) controller.
8.9.5 Software
[0474] Each of the systems of the invention includes software. The
software provided on a storage medium is one aspect of the
invention. Examples of suitable storage mediums include magnetic
storage, optical storage, phase-change memory, holographic storage,
molecular memory storage, battery or capacitor-backed SRAM and
flash memory storage. The software may be loaded in memory and/or
in a processor. A system in which software of the invention is
present in memory and/or a processor and/or a storage medium is
also an aspect of the invention.
[0475] The software of the invention may be written in any of a
variety of programming languages, such as Visual C, Java and/or
Python. The system may include an interpreter for translating
droplet manipulation and other instructions from the high-level
language into an intermediate language for execution by the
processor. Alternatively, software written according to the
invention may be compiled into machine language using a compiler.
The software interpreter and compiler for the language of the
invention are themselves novel aspects of the invention. As such,
all forms of data storage, memory, and processors containing the
interpreter and/or compiler are aspects of the invention.
[0476] The system can be programmed to execute a wide variety of
protocols involving any number of droplet manipulations. Multiple
droplets can be independently and simultaneously manipulated on a
single droplet microactuator. The capacity to independently
manipulate multiple droplets in parallel enables execution of
complex protocols as a series of basic microfluidic instructions.
Systems are scalable and may control tens, hundreds, thousands or
more parallel droplet manipulations per droplet microactuator. For
example, at any one moment, up to a maximum of every control
electrode on the droplet microactuator may be engaged in a droplet
operation.
[0477] The system can be programmed to enable users to input
instructions for the execution of protocols. Existing protocols may
be monitored and adjusted according to user requirements. Complex
protocols can be implemented in which the outcome of one or more
steps determines the selection of one or more subsequent steps. For
example, a droplet in which a certain measured result is positive
may be transported for further processing, while a droplet in which
a result is negative may be discarded, or vice versa.
8.9.6 Portability
[0478] Referring to FIGS. 19A and 19B, in some embodiments, the
analyzer is provided as a portable device, such as a hand-held
device 1900. FIG. 19A shows the exterior of handheld device 1900
and FIG. 19B shows a slot 1902 for insertion of a droplet
microactuator (not shown), an optical sensor 1904 for sensing
optical signals from the droplet microactuator, and a lid latch
1906, which may be coupled to the system to indicate whether the
lid is open or closed. It is envisioned that the portable analyzer
may also be a tabletop device. The portability of the droplet
microactuator systems of the invention facilitates point of care or
point of sample collection use in a wide variety of settings in
clinics, operating rooms, emergency rooms, small laboratories, and
in the field (emergency response teams, accidents, disasters,
battlefield, bioterrorism sites etc.) for rapid diagnostics that
can lead to quick turn around times in critical situations.
8.10 User Interface
[0479] The droplet control system includes droplet control software
programmed to display a droplet control interface for controlling
droplet operations on the droplet microactuator, controlling the
sensor, when present, and controlling other hardware associated
with the droplet control system. The system may also include
software to facilitate creation of a set of software or computer
useable instructions for controlling droplet microactuator system
functions, such as droplet operations and/or sensor operations.
[0480] As illustrated in FIG. 20, the system may include a user
interface 2000. The user interface is described further in related
U.S. Patent Application No. 60/806,412, entitled "Systems and
Methods for Droplet Microactuator Operations," filed on Jun. 30,
2006, the entire disclosure of which is incorporated herein by
reference. The user interface may display a map 2001, preferably an
interactive map, of a droplet microactuator. The map may be used to
interact directly with the droplet microactuator to manipulate
droplets on the droplet microactuator to conduct a fluid loading
protocol according to the invention. The map may be used in a
virtual mode to manipulate virtual droplets 2011 in a programming
mode to develop and record subroutines for controlling droplet
microactuator functions and related hardware.
8.10.1 Droplet Control System and User Interface
[0481] The droplet control system includes droplet control
software. The droplet control software is programmed to display a
droplet control interface for controlling droplet operations on the
droplet microactuator, controlling the sensor, when present, and
controlling other hardware associated with the droplet
microactuator system. The droplet control software permits a user
to manipulate droplets on a droplet microactuator via a software
driven user interface. As described above, an example of such an
interface is illustrated in FIG. 20. Among other things, the user
interface may permit a user to view information about a droplet
microactuator. The user interface may also facilitate input by the
user which controls functions of the droplet microactuator and
associated devices, such as associated sensors.
[0482] With respect to controlling droplet operations on a droplet
microactuator, the software is programmed and the system is
configured to, among other things, drive control and reference
electrodes on the droplet microactuator to conduct the droplet
operations. Droplet operations, which are discussed further in
Section 8.8 above, are effected by applying a voltage to selected
electrodes. The software and system may be configured to permit
software loaded in the processor to control activation of the
selected electrodes by controlling the operation of relays
associated with the electrodes.
[0483] As shown in FIG. 20, the user interface 2000, which is
displayed on an output device, may be programmed to display a
graphical illustration or map 2001 of a droplet microactuator
design. The map 2001 may be based on a matrix or other
configuration that defines the position of each of the control
electrodes and/or reservoirs. Components of the map may be
differentiated by appearance, e.g., by shape, color, brightness,
symbols, icons, etc. For example, in the map displayed in FIG. 20,
unactivated droplet manipulation electrodes 2002 can be shown in a
first color (such as gray), activated droplet manipulation
electrodes and reservoirs 2003 can be shown in a second color (such
as red), and unactivated reservoirs 2004 can be shown in a third
color (such as blue).
[0484] In a simple embodiment, the matrix is defined in a control
file which identifies a row and column for each electrode and/or
reservoir. When a control file is loaded, the system reads in the
matrix definitions and displays the corresponding map of the matrix
on the user interface.
[0485] The interface may display information about components of
the map, which may also be stored in the control file. In one
embodiment, the system displays information about a component when
it is moused over, selected, or otherwise electronically identified
by a user. Information displayed may, for example, include some or
all of the following information: [0486] component type, e.g.,
droplet manipulation electrode, reagent reservoir, sample
reservoir, etc.; [0487] electrical connectivity information, e.g.,
electrode enumeration, grounds, pinout number etc.; [0488]
adjacency relationships, e.g., in a polygonal electrode
arrangement; [0489] representative geometry, for rendering the map
in the user interface; [0490] design notes and/or other comments;
[0491] part numbers; [0492] column and/or row position.
[0493] The system may also record the history of the activation of
each electrode, so that the user may track the number of times an
electrode has been activated. History information may, for example,
be displayed by mousing over or selecting an electrode. The system
may be programmed to accept input from a user instructing history
information to be displayed simultaneously for all electrodes.
[0494] To facilitate user interaction, a moused over or selected
electrode 2002 or other component may also cause the electrode or
other component to be highlighted on the droplet microactuator map.
This capability permits a user who is directly controlling droplet
microactuator operations to review information about each potential
step by mousing over the droplet microactuator component prior to
actually selecting and activating the droplet microactuator
component. The system may be programmed to highlight a moused over
component and a selected component differently so that a user may
differentiate between the two.
[0495] The system may include a means 2007 for permitting a user to
select the mode of operation, e.g., select between a virtual or
programming mode in which a program can be written for controlling
a droplet microactuator, and an operation mode in which droplets
are controlled directly on a droplet microactuator.
[0496] The system may include a means 2012 for permitting a user to
select a droplet microactuator design for display. Alternatively,
data identifying the droplet microactuator design may be included
as a component of the droplet microactuator assembly or cartridge
accessible by the system upon coupling of the droplet microactuator
assembly or cartridge to the system.
[0497] It should be noted that in some designs, more than one
electrode may be coupled to the same electrical output. Such
designs can be used to simplify the design of the droplet
microactuator. In such designs, selecting or mousing over one
electrode from a common set may result in selection, highlighting
and activation of all electrodes in the set.
[0498] Thus, in one embodiment, the system is programmed so that
when a user selects an unactivated electrode 2002 on a
microactuator map 2001, the system activates the electrode. For
example, the system may be programmed and configured so that
clicking on a representation of an electrode on the map causes a
voltage to be applied to a corresponding actual electrode on the
droplet microactuator, thereby activating the selected electrode.
In this way, a user can directly manipulate droplets on the droplet
microactuator using the interface.
[0499] The droplet control system may permit a user to transport a
droplet by sequentially clicking on a series of adjacent
electrodes. Similarly, the system may permit a user to transport a
droplet by selecting a virtual on-screen droplet 2011 and dragging
the droplet to a virtual electrode at a desired location on the
droplet microactuator map. Moreover, the system may permit a user
to transport a droplet by selecting a virtual on-screen droplet
2011, then clicking a virtual electrode at a desired location on
the droplet microactuator map. Other droplet microactuator
components may be similarly controlled via a user interface.
[0500] The system may be programmed to display a representation of
the electrical control lines 2005 electronically coupled to the
droplet microactuator components, so that when a user mouses over
and/or selects a component, the system highlights the electrical
signal that is activated as a result of being mapped to the
component.
[0501] The droplet microactuator may be visually monitored, e.g.,
using a microscope and video capture device. The user interface may
be programmed to display a real-time image of the droplet
microactuator from the video capture device. Further, the droplet
microactuator map may be superimposed over the real-time droplet
microactuator image so that a user can visualize droplet operations
on the droplet microactuator as he or she interacts with the
droplet microactuator via the user interface.
[0502] Similarly, the system may be programmed to display virtual
droplets 2011 on the droplet microactuator map which illustrate
actual behavior of droplets on a droplet microactuator which is
being controlled by the system, and/or the system may be programmed
to display virtual droplets 2011 on the droplet microactuator map
which illustrate predicted behavior of droplets on a droplet
microactuator, even though a droplet microactuator is not being
directly controlled by the system.
[0503] The system may also be programmed to effect an "inverse
output" 2006 operation. In typical operation, the droplets are
constantly connected to a ground voltage/ground line. In the
"inverse output" operation, the signals are inverted so that the
droplet is at a high voltage and the electrodes are activated by
setting them to ground potential. In other words, the "inverse
output" operation switches the polarity of the signals.
[0504] The system may also facilitate creation of a set of software
or computer useable instructions for controlling droplet operations
on the droplet microactuator and controlling other functions of a
droplet microactuator and related hardware. The software
instructions may, for example, include instructions for executing a
protocol for processing and analyzing a sample and outputting
results of the analysis. The system may facilitate writing programs
for controlling droplet microactuator functions and related
components, such as sensor components without interacting with an
actual droplet microactuator.
[0505] The system may, for example, include means for permitting a
user to create a program with a set of instructions for execution
by the droplet microactuator. Examples of suitable instructions
include: [0506] "on" for identifying electrodes that are to be
actuated; [0507] "frequency" to set the rate at which the steps are
executed, e.g., the timing of electrode activation/deactivation;
[0508] "wait" to permit the instructions to pause for a
predetermined period; [0509] "loop" to loop steps in the program;
[0510] "voltage" to set the voltage being applied to the
outputs.
[0511] Instructions can be provided as a byte-coded language which
includes instructions needed to conduct droplet manipulations and
control other aspects of the system. The instructions prepared by
the system can be recorded in the assembly language and assembled
into byte codes. The byte codes can be loaded into a system of the
invention, e.g., a protocol execution system, for execution. The
system may include a software interpreter for interpreting the
language for execution, e.g., in a protocol execution system.
[0512] In a preferred embodiment, the system displays a series of
buttons or icons 2008 that can be selected to add, insert, update,
modify or delete instructions from a subroutine. The buttons or
icons may, as appropriate, be accompanied by fields 2009 for the
entry of parameters associated with the instructions. For example,
by clicking the "add" button, a command can be added at the end of
a subroutine. By clicking an "insert" button, a command can be
inserted within a subroutine. By clicking a "modify" button, a
command present in a subroutine can be modified. By clicking a
"delete" button, a command can be deleted. Further, a display field
2010, which may be editable, may be included for viewing, entering
and/or editing code.
[0513] The system may display a simulated execution of a subroutine
on the droplet microactuator map, which outputs to the user a
visual display of the effects of the command series selected. In
other words, in a simulated execution mode, the software executes
the steps of a subroutine but does not send an electrical signal to
the droplet microactuator. In a preferred simulation mode,
simulated droplets are displayed on the screen to illustrate to the
user the actual effect of the program. In this way, a user can
readily troubleshoot a subroutine without requiring interaction
with a droplet microactuator.
8.10.2 Protocol Execution System and User Interface
[0514] The invention provides a protocol execution system. The
protocol execution system includes protocol execution software
programmed to facilitate execution of a set of software
instructions for loading fluid, controlling droplet operations on
the droplet microactuator and/or other functions of a droplet
microactuator and related hardware. The protocol execution system
provides the ability to execute protocols on a free-standing
system, typically a portable or handheld system.
[0515] The protocol execution system is configured to control the
droplet microactuator and any associated components. Pre-programmed
instructions may be loaded into the controller which controls the
system and any associated components. The protocol execution system
may include various components for permitting a user to provide
input to and obtain output from the processor. The human-machine
interface may be facilitated using a HMI board. The HMI board
typically includes a controller and various electronic components,
such as buses and ports for electronically coupling input and
output devices with the processor.
8.11 Sensors
[0516] The droplet microactuators and systems include sensors for
measuring droplet properties, such as physical properties, chemical
properties, and electrical properties. In some embodiments, the
sensors will include a sensing element arranged to interact with a
droplet and/or a signal from a droplet; a transducing element,
which converts output from a sensor into a measurable signal; a
means for transmitting the signal to the processor. The processor
may convert the signal into an output recognizable to a user.
[0517] The sensor element may be a component of the droplet
microactuator, e.g., mounted on a top or bottom plate, positioned
in the interior space of a droplet microactuator between top and
bottom plates, or manufactured as an integral component of the
droplet microactuator, e.g., an integral component of top or bottom
plates. In other embodiments, the sensor element may be exterior to
the droplet microactuator but arranged within the system in a
manner which permits the sensor to receive a signal from on the
droplet microactuator, e.g., from a droplet on a droplet
microactuator. For example, a sensor element for sensing photons
may be arranged to receive photons from a droplet on a droplet
microactuator. Where the system has a top plate capable of
transmitting photons from a droplet, the sensor may be arranged in
proximity to the top plate for sensing the photons. Where the
system has a top plate not capable of transmitting photons from a
droplet, the top plate may be provided with a window capable of
transmitting photons, and the sensor may be arranged in proximity
to the window for sensing the photons.
[0518] Illustrative examples of sensor configurations are provided
in FIGS. 21A-21D wherein the sensors may be provided in association
with a bottom plate 2102, a top plate 2104, and electrodes 2106.
FIG. 21A illustrates an optical sensor which may include use of a
setup including an LED 2108 and a photodiode 2110 for monitoring
absorbance. FIG. 21B illustrates a luminometric sensor which may
include use of a photomultiplier tube (PMT) 2112. FIG. 21C
illustrates a potentiometric sensor 2114 which typically functions
based on the measurement of a potential under no current flow. FIG.
21D illustrates an amperometric sensor 2116 which typically
functions by the production of a current when a potential is
applied between two electrodes.
[0519] It is important to keep in mind that, as noted elsewhere in
this disclosure, the droplet microactuator may be supplied as a
separate component which can be coupled to a system by a user.
Where sensors are exterior to the droplet microactuator, those
sensors may in some embodiments be aligned such that upon coupling
to the droplet microactuator system, the sensing elements are
appropriately aligned to detect signals from the droplet
microactuator, e.g., the photon sensor is aligned with the
appropriate window and/or with the appropriate location on the
droplet microactuator where the sensing step will be accomplished
in the course of a droplet protocol.
[0520] In various embodiments, the droplet microactuator and/or
system may be configured with sensor components enabling the
implementation of one or more types of sensing. Examples of
suitable sensing types include physical sensing, electrochemical
sensing, and optical sensing.
8.11.1 Physical Approaches
[0521] A droplet microactuator and/or system of the invention may
include one or more physical sensors arranged to sense a property
of a droplet on a droplet microactuator. Examples of physical
sensing include temperature and droplet size (e.g., by thermally
measuring the footprint of the droplet).
8.11.2 Electrochemical Approaches
[0522] The droplet microactuator system of the invention makes use
of a variety of optical detection approaches. A droplet
microactuator and/or system of the invention may include one or
more electrochemical sensors arranged to sense a property of a
droplet on a droplet microactuator. Examples of suitable
electrochemical sensing types include potentiometric sensors,
amperometric sensors, voltametric sensors, and conductometric
sensors. The various components of the sensors (e.g., electrodes,
counter electrodes, reference electrodes, etc.) may be provided on
the same or separate substrates, arranged to permit contact with a
droplet on the droplet microactuator. For example, in embodiments
in which the droplet microactuator includes two substantially
parallel substrates, various components of the sensor assemblies
may be comprised on one or both of the substrates. In some
embodiments, an electric circuit may be used to amplify signals
into a measurable voltage. Various aspects of these approaches are
discussed in the ensuing sections.
8.11.2.1 Amperometry Sensor
[0523] The droplet microactuator device or system may include an
amperometry sensor and an electrical source arranged to permit a
droplet on the droplet microactuator to be transported into contact
with electrical source and the sensor to permit detection of
electric current flowing through the droplet.
8.11.2.2 Potentiometry Sensor
[0524] The droplet microactuator device or system may include a
potentiometry measuring and reference electrode arranged to permit
a droplet on the droplet microactuator to be transported into
contact with the measurement and reference electrodes to permit
measurement of equilibrium electrode potential of a droplet.
8.11.3 Optical Approaches
[0525] The droplet microactuator system of the invention makes use
of a variety of optical detection approaches.
[0526] A droplet microactuator and/or system of the invention may
include one or more optical sensors arranged to sense a property of
a droplet on a droplet microactuator. Examples of optical sensing
include absorbance, chemiluminescence, and fluorescence. Optical
sensors may in some cases be accompanied with an appropriate light
source, e.g., for exciting fluorescence or conducting absorbance
measurements. These sensors may be provided as components mounted
on a droplet microactuator and/or as integral parts of a droplet
microactuator, e.g., using semiconductor manufacturing
techniques.
[0527] Optical sensors may include various optics designed to
direct optical signals, and may be coupled to various image
processors for analyzing optical images. For example, droplet size
may be detected by processing an image of a droplet. Similarly,
droplet size may be obtained by measuring a thermal footprint of
the droplet. Electrical sensors may also be used to measure droplet
size, e.g., by measuring impedance of the droplet footprint.
[0528] In some cases, surfaces of the droplet microactuator may be
modified to enhance optical sensing. For example, electrodes with
reflective surface finishes may be used to facilitate optical
measurements of droplets. The use of reflective electrodes
increases the path length for absorbance measurements and is also
compatible with reflectance spectroscopy. For auto-fluorescent
substrates, such as PCB, coating a droplet microactuator surface
with a non-fluorescent coatings can be used to provide a
non-fluorescent detection zone.
[0529] Various aspects of these approaches are discussed in the
ensuing sections.
8.11.3.1 Photosensor
[0530] The droplet microactuator device or system may include an
absorbance detection components including a light source and a
photosensor arranged to permit a droplet on the droplet
microactuator to be transported into proximity with the light
source and photosensor such that light or energy passing through
the droplet can be detected by the photosensor.
[0531] The droplet microactuator device or system may include
chemiluminescence detection components including a photosensor
(such as a photodiode, avalanche photodiode, photomultiplier tube)
or photon sensor (such as a photon-counting photomultiplier tube)
arranged to permit a droplet on the droplet microactuator to be
transported into proximity with the photosensor or photon sensor
such that photons emitted by chemical species in the droplet can be
detected by the photosensor or photon sensor.
8.11.3.2 Fluorescence Sensor
[0532] The droplet microactuator device or system may include
fluorescence detection components including a light excitation
source with appropriate filters, if necessary, and a photosensor
(such as a photodiode, avalanche photodiode, photomultiplier tube)
or a photon sensor (such as a photon-counting photomultiplier tube)
with appropriate filters and dichroic mirrors, if necessary,
arranged to permit a droplet on the droplet microactuator to be
transported into proximity with the light excitation source and the
photosensor or photon sensor such that photons emitted by
fluorescent species in the droplet can be detected by the
photosensor or photon sensor.
8.11.3.3 Surface Plasmon Resonance
[0533] In another embodiment, surface plasmon resonance (SPR)
sensing is employed to detect interactions between an antibody and
any target analyte. SPR sensing is useful to detect and quantify
such interactions. Typically, one interactant in the interactant
pair (i.e., antibody or analyte) is immobilized on an SPR-active
gold surface on a glass substrate. The interactant may be
immobilized using a droplet-based approach wherein a droplet is
transported into contact with the gold surface to deposit the
interactant thereon. A droplet including the other interactant may
be transported into contact with the immobilized interactant,
thereby permitting the other interactant to bind to the immobilized
interactant. When light (e.g., visible or near infrared) is
directed through the glass substrate and onto the gold surface at
angles and wavelengths near the surface plasmon resonance
condition, the optical reflectivity of the gold changes very
sensitively with the presence of biomolecules on the gold surface
or in a thin coating on the gold. The optical response may be
highly sensitive due to the fact that it involves an efficient,
collective excitation of conduction electrons near the gold
surface. The extent of binding between the solution-phase
interactant and the immobilized interactant may be observed and
quantified by monitoring this reflectivity change. The invention
also includes a droplet microactuator including a gold surface
thereon, and a path or network of electrodes arranged to permit the
execution of droplet manipulations sufficient to bring a droplet
into contact with the gold surface. Further, the invention includes
a system including such droplet microactuator and further including
a light source capable of directing light onto the gold surface at
angles and wavelengths near the surface plasmon resonance
condition. Similarly, the invention includes a system including
such a droplet microactuator and further including a means for
detecting changes in reflectivity of the gold surface. Moreover,
the invention includes a droplet microactuator device and/or system
having loaded thereon reagents sufficient to conduct some or all
steps of an SPR protocol.
8.11.3.4 Raman Spectroscopy
[0534] In one embodiment, the droplet microactuator and/or system
includes Raman spectroscopic detection capability. In general, this
capability includes a Raman signal-generating light source, a Raman
signal detection surface, and a Raman spectrophotometer.
[0535] The Raman signal generating light source may, for example,
be a monochromatic light, e.g., a laser source with excitation in
the visible wavelength range. The light source is arranged to
irradiate a Raman signal detection surface on a droplet
microactuator. The surface may, for example, be a surface of the
droplet microactuator and/or a surface of a particle on a droplet
microactuator. For example, the surface may be the surface of a
particle in a droplet on a droplet microactuator. The droplet
microactuator may have the capability of conducting droplet
operations using a droplet including such particles in order to
effect various protocols which employ Raman signal detection
methods.
[0536] The Raman signal detection surface may include any surface
appropriate for Raman scattering. Examples include gold or silver
surface. The surface may be roughened. The droplet microactuator
may in some cases include multiple metallic surfaces (e.g.,
surfaces of the droplet microactuator, beads, particles,
nanoparticles, etc.), including surfaces labeled with a different
Raman reporter molecules. Antibodies or analytes bound to the
surface may be identified by the characteristic Raman spectra of
the Raman reporter molecules. The Raman detection surface may, for
example, be an electrode, a coating on the electrode, or a layer on
any chip surface. In operation, a droplet is positioned using
droplet operations on the Raman detection surface, and is
irradiated with a laser beam. Scattered light from the irradiated
surface is collected with a spectrometer. In another embodiment,
the Raman detection surface is a particle in a droplet on a droplet
microactuator. The particle may, for example, be a nanoparticle,
such as a silver or gold nanoparticle. For example, silver
nanoparticles can be prepared as monodispersed colloidal
suspensions, which can be manipulated on a droplet microactuator
using droplet operations. In some embodiments, the particles may be
aggregated into clusters using aggregation additives, such as
inorganic salts such as sodium chloride or sodium nitrate, acids
such as nitric or hydrochloric or organic amines such as
poly-L-lysine. These aggregation additives can be combined with a
droplet including the sample and the particles using droplet
operations, e.g., using droplet operations to combine a droplet
including the aggregation additive with a droplet including the
particles and sample. Surfaces of the droplet microactuator
associated with the Raman spectroscopic region are selected to
minimize the background fluorescence signal.
[0537] A Raman spectrophotometer is arranged to detect Raman
scattered light emitted from the sample droplet. The Raman
spectrophotometer may be integral with the droplet microactuator
arranged exterior to the droplet microactuator in a manner which
permits it to detect Raman scattered light emitted from the sample
droplet on the droplet microactuator.
[0538] In operation, a droplet microactuator is provided having a
Raman detection surface thereon. An analyte is brought into
association with the Raman detection surface using droplet
operations. The surface is irradiated with a Raman signal
generating light source. Raman scattered light signals are detected
correlated with expected signals in order to determine the identity
and/or quantity of an analyte.
[0539] In another embodiment, surface-enhanced Raman scattering
(SERS) is employed to detect interactions between an antibody and
any target analyte. In general, this method involves monitoring an
analyte mediated binding event in a sample droplet which includes
the analyte, a specific binding member, a Raman-active label, and
is in contact with a surface, such as a bead or a surface of the
droplet microactuator, and which is capable of inducing a
surface-enhanced Raman light scattering. The sample droplet is
illuminated with a radiation sufficient to cause the Raman-active
label in the test mixture to emit a detectable Raman spectrum. The
differences in the detected surface-enhanced Raman scattering
spectra are dependent upon the quantity of the analyte present in
the test mixture. The presence and/or quantity of the analyte in
the sample droplet may be determined by monitoring the Raman
scattering spectra. The invention includes a droplet microactuator
device and/or system having loaded thereon reagents sufficient to
conduct some or all steps of an SERS protocol.
[0540] In a related embodiment, the invention provides a method for
determining the presence or quantity of an analyte in a sample
droplet by monitoring an analyte-mediated ligand binding event on a
droplet microactuator. The method generally includes reacting the
analyte with an antibody coupled to a Raman active label. The
reaction is conducted using droplets on a droplet microactuator and
is effected under conditions permitting specific binding of the
antibody to the analyte, if present, to yield a first complex in
the sample droplet. Sequentially or simultaneously the first
complex is contacted with a surface capable of inducing a
surface-enhanced Raman light scattering and having attached thereto
an antibody specific for the analyte to form a second complex. The
second complex is illuminated with a radiation sufficient to cause
the Raman-active labels in the complex to produce a detectable
Raman spectrum. Differences in the surface-enhanced Raman
scattering spectra are indicative of the presence and/or quantity
of the analyte present in the test mixture.
[0541] A variety of surfaces may be appropriate for the
droplet-based SERS protocols of the invention. Examples include
roughened metal electrodes, aggregated, films, metal islands of
different morphology, semicontinuous films near the percolation
threshold, and vacuum-evaporated nanostructured metal films.
Accordingly, the invention includes a droplet microactuator
including an SERS substrate. The droplet microactuator is suitably
arranged such that a droplet may be transported along a path or
network of electrodes into contact with the SERS substrate.
[0542] In DNA detection methods of the invention, a Raman label may
be used. A label may be a non-sequence specific intercalator or a
specific label covalently attached to a unique probe sequence.
Negatively charged labels may require the use of a charge
neutralizing agent, such as spermine, to facilitate association of
the label with a negatively charged surface, such as silver
nanobeads with a citrate surface layer. Aggregating agents may also
be used in order to improve signal. Spermine may also serve as an
aggregating agent.
8.11.3.5 Multisensor Capabilities
[0543] Preferred sensors are sensors for detecting absorbance,
fluorescence, chemiluminescence, as well as potentiometric,
amperometric, and conductometric sensors. The droplet microactuator
device and/or system of the invention includes one or more of these
detection capabilities. In one embodiment, a droplet microactuator
includes components for facilitating 2 or more of these detection
methods on a single droplet microactuator. In another embodiment,
the droplet microactuator includes one detection module, but the
system is programmed to conduct more than one test using the
module. In this embodiment, processed sample droplets requiring
testing are sequentially moved into position for testing. Thus,
multiple samples may be multiplexed over a detection spot where a
single sensor is used.
8.11.4 Sensor Electronics
[0544] The detection capabilities may be provided as one or more
components of a sensor board. The sensor board may include one or
more sensors. The sensor board may include additional electronic
circuitry such as amplifiers, A/D converters, read-out circuits and
the like for conditioning or amplifying the signal received from a
droplet. The sensor board may include control elements or other
off-droplet microactuator components of the detection protocol,
such as control of motors for moving components of the system.
[0545] In one embodiment, the sensor board includes a servo motor
controller for controlling a servo motor that moves a magnetic
field source into and out of proximity with the droplet operation
surface, thereby applying/removing the magnetic field to/from the
droplet microactuator. This embodiment is useful for manipulating
magnetically responsive materials. The sensor board may also
include power supply elements and communication elements, including
without limitation, elements required to electronically couple the
sensor components or control components of the board to the
processor.
[0546] The optical detection location may include specialized
coatings, electrode designs, or other features that facilitate
optical detection. For example, the detection spot may include a
specialized pad and/or coating that facilitates its operation as a
background surface for optical measurement.
[0547] In certain embodiments, such as nucleic acid amplification
applications, the preferred optical detection method is
fluorescence quantitation. In such embodiments, the detection spot
may be selected to shield background fluorescence present in the
microactuator substrate or coatings disposed on the microactuator
substrate. For example, in one embodiment, the microactuator is
comprised of a printed circuit board substrate and the detection
spot is comprised of a gold pad which shields the background
fluorescence of the substrate from the sensor thereby facilitating
fluorescent measurement of a droplet positioned on the pad. The pad
may be formed in a metal layer disposed directly on the substrate
or disposed on an intervening layer disposed on the substrate.
[0548] Preferably, the metal layer in which the pad is formed
should be disposed on top of any layers exhibiting significant
background fluorescence. In one embodiment the pad is disposed
directly on a printed circuit board substrate being formed in the
same metal layer as the electrodes for controlling the droplet. In
this embodiment, the dielectric material (which may also exhibit
background fluorescence) may be disposed above the metal layer and
is selectively removed from the detection pads, but not the control
electrodes.
[0549] Thus, a low background fluorescence detection spot may be
achieved through a combination of selective removal of fluorescent
material above the detection pad and optical shielding of
fluorescent material located below the pad. The pad is preferably
designed to minimize its interference with other droplet
microactuator functions. In the embodiment described above, the pad
may be formed in the same metal layer as the control electrode but
is separate and electrically distinct from the control electrodes.
The pad therefore
8.11.5 Detection Approaches
[0550] The invention provides a variety of approaches for
sensing/detecting signals or attributes of droplets. Many of these
approaches are described elsewhere in this specification. This
section describes additional approaches that may be useful in
various settings.
[0551] An advantage of the droplet microactuator approach of the
invention includes the ability to decouple reaction steps in a
particular assay. Many biochemical assays use common end reactions
to generate a color, light or other detectable quantity.
Droplet-based protocols of the invention can be used to combine the
assay droplet with a droplet containing the end reaction reagents
at the point of detection. Decoupling of the assay steps permits
each to be separately optimized and separation of the steps in time
provides greater flexibility when one of the reaction steps is rate
limiting. For example chemiluminescence assays typically have
better results at a basic pH. For an assay which is optimal at an
acidic pH assay reaction can be completed first at the acidic pH,
and the light generation aspect of the reaction can be performed at
a basic pH.
[0552] The droplet microactuators of the invention are useful in
the study of rate kinetic reactions. Sample droplets can be
periodically dispensed from a reservoir in which a reaction is
occurring. The droplets can then be individually analyzed to
determine the time course of the reaction. The droplets can be
analyzed in real-time or mixed with another reagent for later
analysis. Electrowetting may also be used to rapidly mix droplets
for the purpose of studying fast reaction kinetics.
[0553] Changes in viscosity of a droplet can be measured as a means
for assessing the state of a chemical reaction inside the droplet.
For example, a coagulant can be added to a droplet of blood
followed by transporting the droplet and monitoring of the ease of
transport of the droplet. Greater degrees of coagulation would make
transport of the droplet more difficult which can be detected as
used as a measure of the degree of coagulation.
[0554] Preferred sensors include optical sensors for sensing
optical signals, such as absorbance, fluorescence, and
chemiluminescence, and electrochemical sensors for sensing
electrochemical properties, such as potentiometric properties,
amperometric properties, conductometric properties. Accordingly,
the droplet microactuator system of the invention includes
components arranged to facilitate detection of one or more of these
properties. In one embodiment, 2 or more of these properties are
detected on one or more droplets on a single droplet microactuator
or otherwise accomplished using a single droplet microactuator
system. In another embodiment, the droplet microactuator includes
one sensor of a particular type, and the system is programmed to
conduct more than one test using the sensor. In this embodiment,
processed sample droplets requiring testing are sequentially moved
into position for testing, i.e., moved into sufficient proximity to
the requisite sensor to enable detection. Thus, multiple samples
may be multiplexed over a detection spot for detection by a single
sensor. Multiple sensor types may be supplied on a single droplet
microactuator using this approach.
[0555] The droplet microactuator system may in some embodiments be
configured to deposit a droplet or sample to a location that is
exterior to the droplet microactuator for detection. For example a
droplet including (or potentially including) an analyte can be
deposited on a substrate for MALDI-TOF analysis.
[0556] Droplets can be cyclically transported past a common
detection point in proximity to an appropriate sensor to allow
multiple reactions to be simultaneously monitored. For example the
droplet microactuator can include two or more "tracks" that connect
high and low temperature zones in a flow-through PCR reaction
chamber. A single detector is placed at the intersection of the
tracks. Droplet traffic can be timed to cause droplets to
sequentially pass over the detection spot.
[0557] Examples of assays suitable for execution in the
droplet-based protocols of the invention on the droplet
microactuator of the invention include optical assays, such as
absorbance assays, fluorescence assays, bioluminescence assays and
chemiluminescence assays; and electrochemical assays, such as
potentiometric assays, amperometric assays, and conductometric
assays. For example, various combinations of one or more of the
foregoing assay types can be used to identify and/or quantify one
or more analytes, such as proteins, enzymes, nucleic acids,
metabolites, electrolytes, gasses (e.g., blood gases) and
hematocrit. A system of the invention may be programmed to conduct
on a single droplet microactuator various combinations of these
assay types.
[0558] In one embodiment, a single droplet microactuator or system
includes detection capabilities for 2, 3, 4, 5, 6 or more different
kinds of assays. For example, the droplet microactuator device,
system and/or other components of a droplet microactuator system
may separately or together include one or more detection
components, such as components for amperometry, potentiometry,
conductometry, absorbance, chemiluminescence, fluorescence, and/or
temperature. Further, a droplet microactuator system may be
programmed to execute assay protocols for conducting 2, 3, 4, 5, 6
or more different kinds of assays on the same or multiple samples
or sample types.
[0559] Within the droplet microactuator, the droplet manipulation
components and the detection components may in some embodiments be
decoupled by providing them on separate substrates. Similarly,
various detection components may be provided as part of a droplet
microactuator device or system, but separate from the droplet
microactuator. Thus, for example, a sensor may be provided on a
cartridge to which the droplet microactuator is coupled. The
coupling is arranged so that when the droplet microactuator is
coupled to the cartridge, suitable components are aligned to permit
detection. Thus, for example, a photon sensor may be aligned with a
window or other transparent substrate so that when the droplet
microactuator is properly mounted on the cartridge, photons emitted
from a droplet on the droplet microactuator may pass through the
window or substrate for detection by the photon sensor. Similarly,
where a light source is necessary to cause fluorescence of a
molecule in a droplet on the droplet microactuator, the light
source may be mounted to the cartridge or other component of the
droplet microactuator device or system and aligned so that the
light source can reach the droplet to produce the desired
fluorescence.
[0560] In one embodiment, the droplet microactuator includes
electrodes for performing electrochemistry. Electrodes can be
patterned onto the electrowetting substrate to permit
electrochemical measurement of droplets in contact with the
electrodes. In a two-substrate droplet microactuator, the
electrodes for performing electrochemistry can be formed either or
both substrates. In some embodiments, transport electrodes and
electrochemical measurement electrodes are provided on different
substrates. The electrodes may include membranes for fabricating
ion-selective analyses.
8.12 Other Methods
[0561] The invention includes a method in which components of a
bench-top system are offered to or provided to a customer in
exchange for consideration. In one embodiment, the components
offered to or provided to the customer do not include the PC. The
software of the invention may be provided to the user on a storage
medium or made available for download via a network, such as the
Internet. The user may obtain other components of the system,
couple the components to a PC, load the software on a PC, and
thereby assemble system of the invention.
[0562] The invention includes a method in which a bench-top system
is used to generate code for executing a protocol. Code is uploaded
into a separate system, such as a portable or handheld system,
which is offered to or provided to a customer in exchange for
consideration. The user may use the system for executing the
protocol.
[0563] The invention also includes a method in which programming
and/or system control is effectuated remotely via a network, such
as a telephone system or the internet. Thus, for example, a system
may be sold to a user, a programmer may connect to the system via a
user interface displayed via the Internet to control the system,
create programs using the system, load programs on the system,
and/or repair programs on the system. As another example, the
invention includes a process whereby a remote user accesses a
droplet microactuator via a network and performs one or more
droplet manipulations on the system.
8.13 Kits
[0564] A further aspect of the invention is a kit including
reagents, sample collection devices, and/or a droplet microactuator
or cartridge for conducting the methods of the invention.
8.14 Concluding Remarks
[0565] The foregoing detailed description of embodiments refers to
the accompanying drawings, which illustrate specific embodiments of
the invention. Other embodiments having different structures and
operations do not depart from the scope of the present
invention.
[0566] As will be appreciated by one of skill in the art, the
present invention may be embodied as a method, system, or computer
program product. Accordingly, the present invention may take the
form of an entirely hardware embodiment, an entirely software
embodiment (including firmware, resident software, microcode, etc.)
or an embodiment combining software and hardware aspects that may
all generally be referred to herein as a "circuit," "module" or
"system." Furthermore, the present invention may take the form of a
computer program product on a computer-usable storage medium having
computer-usable program code embodied in the medium.
[0567] Any suitable computer useable medium may be utilized. The
computer-usable or computer-readable medium may be, for example but
not limited to, an electronic, magnetic, optical, electromagnetic,
infrared, or semiconductor system, apparatus, device, or
propagation medium. More specific examples (a non-exhaustive list)
of the computer-readable medium would include some or all of the
following: an electrical connection having one or more wires, a
portable computer diskette, a hard disk, a random access memory
(RAM), a read-only memory (ROM), an erasable programmable read-only
memory (EPROM or Flash memory), an optical fiber, a portable
compact disc read-only memory (CD-ROM), an optical storage device,
a transmission medium such as those supporting the Internet or an
intranet, or a magnetic storage device. Note that the
computer-usable or computer-readable medium may even be paper or
another suitable medium upon which the program is printed, as the
program can be electronically captured, via, for instance, optical
scanning of the paper or other medium, then compiled, interpreted,
or otherwise processed in a suitable manner, if necessary, and then
stored in a computer memory. In the context of this document, a
computer-usable or computer-readable medium may be any medium that
can contain, store, communicate, propagate, or transport the
program for use by or in connection with the instruction execution
system, apparatus, or device.
[0568] Computer program code for carrying out operations of the
present invention may be written in an object oriented programming
language such as Java, Smalltalk, C++ or the like. However, the
computer program code for carrying out operations of the present
invention may also be written in conventional procedural
programming languages, such as the "C" programming language or
similar programming languages. The program code may execute
entirely on the user's computer, partly on the user's computer, as
a stand-alone software package, partly on the user's computer and
partly on a remote computer or entirely on the remote computer or
server. In the latter scenario, the remote computer may be
connected to the user's computer through a local area network (LAN)
or a wide area network (WAN), or the connection may be made to an
external computer (for example, through the Internet using an
Internet Service Provider).
[0569] The present invention is described with reference to
flowchart illustrations and/or block diagrams of methods, apparatus
(systems) and computer program products according to embodiments of
the invention. It will be understood that each block of the
flowchart illustrations and/or block diagrams, and combinations of
blocks in the flowchart illustrations and/or block diagrams, can be
implemented by computer program instructions. These computer
program instructions may be provided to a processor of a general
purpose computer, special purpose computer, or other programmable
data processing apparatus to produce a machine, such that the
instructions, which execute via the processor of the computer or
other programmable data processing apparatus, create means for
implementing the functions/acts specified in the flowchart and/or
block diagram block or blocks.
[0570] These computer program instructions may also be stored in a
computer-readable memory that can direct a computer or other
programmable data processing apparatus to function in a particular
manner, such that the instructions stored in the computer-readable
memory produce an article of manufacture including instruction
means which implement the function/act specified in the flowchart
and/or block diagram block or blocks.
[0571] The computer program instructions may also be loaded onto a
computer or other programmable data processing apparatus to cause a
series of operational steps to be performed on the computer or
other programmable apparatus to produce a computer implemented
process such that the instructions which execute on the computer or
other programmable apparatus provide steps for implementing the
functions/acts specified in the flowchart and/or block diagram
block or blocks.
[0572] This specification is divided into sections for the
convenience of the reader only. Headings should not be construed as
limiting of the scope of the invention.
[0573] It will be understood that various details of the present
invention may be changed without departing from the scope of the
present invention. Furthermore, the foregoing description is for
the purpose of illustration only, and not for the purpose of
limitation, as the present invention is defined by the claims as
set forth hereinafter.
* * * * *
References